cis-eQTL summary statistics application

[gaow]

I wonder what people would suggest for storing eg cis-eQTL data, when a variant is in cis with multiple genes. I'm thinking of using INFO to annotate the cis-gene for a variant so there could be multiple lines having the same chr, pos, ref, alt but different INFO on gene, and possibly a different ID as a result of including cis-gene names. Is that the best thing to do?

[hsun3163]

One way of solving this issue I think is to put the GENE as a prefix of the ID, i.e. GENE:CHR:POS:REF:ALT. bcftools have a option to merge multiple vcf file by their ID. As indicated below, bcftools merge -m id test_merged_1.vcf.gz test_merged_2.vcf.gz produce a vcf output that is a full joint of the two individual GWAS_VCF while merging only the rows that corresponding to the same genes.

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20220403
##FORMAT=<ID=STAT,Number=1,Type=Float,Description="Effect size estimate relative to the alternative allele">
##FORMAT=<ID=SE,Number=1,Type=Float,Description="Standard error of effect size estimate">
##FORMAT=<ID=P,Number=1,Type=Float,Description="The Pvalue corresponding to ES">
##INFO=<ID=GENE,Number=1,Type=String,Description="The name of genes">
##FORMAT=<ID=TSS_D,Number=1,Type=Integer,Description="Customized Field TSS_D">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Customized Field AF">
##FORMAT=<ID=MA_SAMPLES,Number=1,Type=Integer,Description="Customized Field MA_SAMPLES">
##FORMAT=<ID=MA_COUNT,Number=1,Type=Integer,Description="Customized Field MA_COUNT">
##FORMAT=<ID=GENE.1,Number=1,Type=Str,Description="Customized Field GENE.1">
##contig=<ID=17>
##bcftools_mergeVersion=1.14+htslib-1.14
##bcftools_mergeCommand=merge -m id test_merged_1.vcf.gz test_merged_2.vcf.gz; Date=Fri Apr  8 15:27:25 2022
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ALL     Ast
17      150509  TIMM22:chr17:150509_T_TA        T       TA      .       PASS    GENE=TIMM22     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                           .:.:.:.:.:.:.:.  -0.0403918:0.0808863:0.617858:-846620:0.185542:135:154:TIMM22
17      150509  NXN:chr17:150509_T_TA   T       TA      .       PASS    GENE=NXN        STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  -0.00313498:0.0608204:0.958923:-829267:0.185542:135:154:NXN
17      150509  GLOD4:chr17:150509_T_TA T       TA      .       PASS    GENE=GLOD4      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  0.125392:0.0864899:0.148077:-632881:0.185542:135:154:GLOD4
17      150509  TLCD3A:chr17:150509_T_TA        T       TA      .       PASS    GENE=TLCD3A     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                           0.023213:0.05232:0.657572:-581903:0.185542:135:154:TLCD3A        0.00764352:0.0869836:0.930031:-581903:0.185542:135:154:TLCD3A
17      150509  VPS53:chr17:150509_T_TA T       TA      .       PASS    GENE=VPS53      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   -0.0357983:0.0440621:0.417124:-571208:0.185542:135:154:VPS53     -0.042744:0.0633347:0.500221:-571208:0.185542:135:154:VPS53
17      150509  AC015853.3:chr17:150509_T_TA    T       TA      .       PASS    GENE=AC015853.3 STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                           0.000276494:0.0194655:0.988676:-372631:0.185542:135:154:AC015853.3       -0.0919213:0.0498577:0.0661356:-372631:0.185542:135:154:AC015853.3
17      150509  C17orf97:chr17:150509_T_TA      T       TA      .       PASS    GENE=C17orf97   STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                           0.0382362:0.0830526:0.645546:-259816:0.185542:135:154:C17orf97   0.0209041:0.0825456:0.80024:-259816:0.185542:135:154:C17orf97
17      150509  RPH3AL:chr17:150509_T_TA        T       TA      .       PASS    GENE=RPH3AL     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                           0.200842:0.0699569:0.00435926:-235745:0.185542:135:154:RPH3AL    0.0131605:0.0674609:0.845449:-235745:0.185542:135:154:RPH3AL
17      150509  RFLNB:chr17:150509_T_TA T       TA      .       PASS    GENE=RFLNB      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.160758:0.0631347:0.0113462:-295430:0.185542:135:154:RFLNB      .:.:.:.:.:.:.:.
17      150509  DOC2B:chr17:150509_T_TA T       TA      .       PASS    GENE=DOC2B      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.35281:0.0581579:3.61441e-09:-31141:0.185542:135:154:DOC2B      .:.:.:.:.:.:.:.
17      151035  TIMM22:chr17:151035_T_C T       C       .       PASS    GENE=TIMM22     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  -0.0264652:0.0814339:0.745396:-846094:0.185542:136:154:TIMM22
17      151035  NXN:chr17:151035_T_C    T       C       .       PASS    GENE=NXN        STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  0.00640265:0.061218:0.916767:-828741:0.185542:136:154:NXN
17      151035  GLOD4:chr17:151035_T_C  T       C       .       PASS    GENE=GLOD4      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  0.124873:0.0870623:0.152445:-632355:0.185542:136:154:GLOD4
17      151035  TLCD3A:chr17:151035_T_C T       C       .       PASS    GENE=TLCD3A     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  0.0116473:0.087552:0.894249:-581377:0.185542:136:154:TLCD3A
17      151035  VPS53:chr17:151035_T_C  T       C       .       PASS    GENE=VPS53      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  -0.0225716:0.0637816:0.72365:-570682:0.185542:136:154:VPS53
17      151035  AC015853.3:chr17:151035_T_C     T       C       .       PASS    GENE=AC015853.3 STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                           .:.:.:.:.:.:.:.  -0.0864778:0.0502172:0.0860018:-372105:0.185542:136:154:AC015853.3
17      151035  C17orf97:chr17:151035_T_C       T       C       .       PASS    GENE=C17orf97   STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                           .:.:.:.:.:.:.:.  0.0104071:0.0830924:0.900404:-259290:0.185542:136:154:C17orf97
17      151035  RPH3AL:chr17:151035_T_C T       C       .       PASS    GENE=RPH3AL     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  0.00852512:0.067905:0.900169:-235219:0.185542:136:154:RPH3AL
17      151041  RPH3AL:chr17:151041_G_A G       A       .       PASS    GENE=RPH3AL     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   .:.:.:.:.:.:.:.  -0.0366692:0.0726522:0.614093:-235213:0.139759:102:116:RPH3AL

Putting Gene information in any other field will results in a mismatched in the output of bcftools merge as indicated below:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20220403
##FORMAT=<ID=STAT,Number=1,Type=Float,Description="Effect size estimate relative to the alternative allele">
##FORMAT=<ID=SE,Number=1,Type=Float,Description="Standard error of effect size estimate">
##FORMAT=<ID=P,Number=1,Type=Float,Description="The Pvalue corresponding to ES">
##INFO=<ID=GENE,Number=1,Type=String,Description="The name of genes">
##FORMAT=<ID=TSS_D,Number=1,Type=Integer,Description="Customized Field TSS_D">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Customized Field AF">
##FORMAT=<ID=MA_SAMPLES,Number=1,Type=Integer,Description="Customized Field MA_SAMPLES">
##FORMAT=<ID=MA_COUNT,Number=1,Type=Integer,Description="Customized Field MA_COUNT">
##FORMAT=<ID=GENE.1,Number=1,Type=Str,Description="Customized Field GENE.1">
##contig=<ID=17>
##bcftools_mergeVersion=1.14+htslib-1.14
##bcftools_mergeCommand=merge --force-samples -Oz -o ...
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ALL     Ast     End     Exc     Inh     Mic    OPC                                              Oli
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=DOC2B      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.35281:0.0581579:3.61441e-09:-31141:0.185542:135:154:DOC2B      0.0131605:0.0674609:0.845449:-235745:0.185542:135:154:RPH3AL                                            0.0905314:0.0607519:0.13737:-829267:0.1875:115:132:NXN   0.322654:0.0587057:7.82572e-08:-31141:0.185542:135:154:DOC2B   0.153654:0.0796014:0.0544352:-31141:0.185542:135:154:DOC2B        -0.156104:0.0762654:0.0414716:-571208:0.185542:135:154:VPS53    0.0973946:0.0790666:0.21891:-571208:0.18599:135:154:VPS53                               -0.0872876:0.0596222:0.144151:-372631:0.185542:135:154:AC015853.3
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=RPH3AL     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.200842:0.0699569:0.00435926:-235745:0.185542:135:154:RPH3AL    0.0209041:0.0825456:0.80024:-259816:0.185542:135:154:C17orf97                                           .:.:.:.:.:.:.:.  0.235547:0.0733648:0.00145601:-235745:0.185542:135:154:RPH3AL   0.0191817:0.0589475:0.745083:-235745:0.185542:135:154:RPH3AL                            0.260086:0.0898613:0.00405531:-632881:0.185542:135:154:GLOD4     0.120468:0.0867618:0.165937:-632881:0.18599:135:154:GLOD4                                               0.0146486:0.0665047:0.825803:-571208:0.185542:135:154:VPS53
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=C17orf97   STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.0382362:0.0830526:0.645546:-259816:0.185542:135:154:C17orf97   -0.0919213:0.0498577:0.0661356:-372631:0.185542:135:154:AC015853.3                                      .:.:.:.:.:.:.:.  0.0701672:0.0804215:0.383579:-259816:0.185542:135:154:C17orf97  0.00290266:0.0797265:0.970979:-259816:0.185542:135:154:C17orf97                         -0.0103012:0.0601909:0.864218:-829267:0.185542:135:154:NXN       0.131247:0.0792178:0.0985242:-829267:0.18599:135:154:NXN                                                0.064894:0.079988:0.417786:-632881:0.185542:135:154:GLOD4
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=RFLNB      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.160758:0.0631347:0.0113462:-295430:0.185542:135:154:RFLNB      -0.042744:0.0633347:0.500221:-571208:0.185542:135:154:VPS53                                             .:.:.:.:.:.:.:.  0.185963:0.0617426:0.00279845:-295430:0.185542:135:154:RFLNB    0.0395762:0.0348068:0.256361:-372631:0.185542:135:154:AC015853.3                        .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. -0.0420404:0.0807668:0.603056:-846620:0.185542:135:154:TIMM22
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=AC015853.3 STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.000276494:0.0194655:0.988676:-372631:0.185542:135:154:AC015853.3       0.00764352:0.0869836:0.930031:-581903:0.185542:135:154:TLCD3A                                   .:.:.:.:.:.:.:.  -0.00795924:0.018865:0.673372:-372631:0.185542:135:154:AC015853.3       0.0414476:0.0453474:0.361389:-571208:0.185542:135:154:VPS53                     .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=VPS53      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   -0.0357983:0.0440621:0.417124:-571208:0.185542:135:154:VPS53     0.125392:0.0864899:0.148077:-632881:0.185542:135:154:GLOD4                                              .:.:.:.:.:.:.:.  -0.0278407:0.0433261:0.520943:-571208:0.185542:135:154:VPS53    0.0240009:0.0733747:0.743801:-581903:0.185542:135:154:TLCD3A                            .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=TLCD3A     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.023213:0.05232:0.657572:-581903:0.185542:135:154:TLCD3A        -0.00313498:0.0608204:0.958923:-829267:0.185542:135:154:NXN                                             .:.:.:.:.:.:.:.  -0.0864781:0.0537734:0.108758:-631943:0.185542:135:154:MRM3     0.0517935:0.0633322:0.414063:-632881:0.185542:135:154:GLOD4                             .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=MRM3       STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   -0.0816996:0.0554548:0.141642:-631943:0.185542:135:154:MRM3      -0.0403918:0.0808863:0.617858:-846620:0.185542:135:154:TIMM22                                           .:.:.:.:.:.:.:.  0.00650789:0.0335411:0.846275:-632881:0.185542:135:154:GLOD4    -0.0678543:0.0538887:0.208872:-829267:0.185542:135:154:NXN                              .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=GLOD4      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.0432869:0.0345032:0.210529:-632881:0.185542:135:154:GLOD4      .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. 0.144339:0.0534027:0.00723412:-829267:0.185542:135:154:NXN              0.106378:0.0667829:0.11215:-846620:0.185542:135:154:TIMM22       .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=NXN        STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.0910669:0.0497962:0.0683413:-829267:0.185542:135:154:NXN       .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. -0.00372898:0.0390022:0.923889:-846620:0.185542:135:154:TIMM22          .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      150509  chr17:150509_T_TA       T       TA      .       PASS    GENE=TIMM22     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.00968499:0.0394625:0.806283:-846620:0.185542:135:154:TIMM22    .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.                                         .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=DOC2B      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.359382:0.0587111:2.65771e-09:-30615:0.185542:136:154:DOC2B     0.00852512:0.067905:0.900169:-235219:0.185542:136:154:RPH3AL                                            0.084474:0.0614837:0.17063:-828741:0.1875:116:132:NXN    0.32539:0.0592411:7.96847e-08:-30615:0.185542:136:154:DOC2B    0.152857:0.080282:0.0577878:-30615:0.185542:136:154:DOC2B -0.143983:0.0776253:0.0645175:-570682:0.185542:136:154:VPS53    0.0609647:0.0797857:0.445357:-570682:0.18599:136:154:VPS53                                      -0.0699054:0.0601662:0.246135:-372105:0.185542:136:154:AC015853.3
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=RPH3AL     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.216399:0.0705649:0.00234519:-235219:0.185542:136:154:RPH3AL    0.0104071:0.0830924:0.900404:-259290:0.185542:136:154:C17orf97                                          .:.:.:.:.:.:.:.  0.247441:0.0739322:0.000912516:-235219:0.185542:136:154:RPH3AL  0.0342429:0.0594218:0.56483:-235219:0.185542:136:154:RPH3AL                             0.252591:0.0914626:0.00607526:-632355:0.185542:136:154:GLOD4     0.0966792:0.0875205:0.270128:-632355:0.18599:136:154:GLOD4                                              0.0427744:0.0669938:0.523607:-570682:0.185542:136:154:VPS53
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=C17orf97   STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.0256586:0.0839348:0.76003:-259290:0.185542:136:154:C17orf97    -0.0864778:0.0502172:0.0860018:-372105:0.185542:136:154:AC015853.3                                      .:.:.:.:.:.:.:.  0.0577114:0.0811823:0.477662:-259290:0.185542:136:154:C17orf97  -0.011526:0.0803935:0.886087:-259290:0.185542:136:154:C17orf97                          -0.00847095:0.0611958:0.889991:-828741:0.185542:136:154:NXN      0.153712:0.0797062:0.0546635:-828741:0.18599:136:154:NXN                                                0.0748392:0.0805954:0.353792:-632355:0.185542:136:154:GLOD4
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=RFLNB      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.173528:0.0637044:0.00679708:-294904:0.185542:136:154:RFLNB     -0.0225716:0.0637816:0.72365:-570682:0.185542:136:154:VPS53                                             .:.:.:.:.:.:.:.  0.201258:0.0621724:0.00133124:-294904:0.185542:136:154:RFLNB    0.0360253:0.0351119:0.305644:-372105:0.185542:136:154:AC015853.3                        .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. -0.0543113:0.0813838:0.50502:-846094:0.185542:136:154:TIMM22
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=AC015853.3 STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   -0.00024197:0.0196687:0.990192:-372105:0.185542:136:154:AC015853.3       0.0116473:0.087552:0.894249:-581377:0.185542:136:154:TLCD3A                                     .:.:.:.:.:.:.:.  -0.00774357:0.0190365:0.684439:-372105:0.185542:136:154:AC015853.3      0.0580043:0.045674:0.205:-570682:0.185542:136:154:VPS53                         .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=VPS53      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   -0.0261631:0.0445435:0.557366:-570682:0.185542:136:154:VPS53     0.124873:0.0870623:0.152445:-632355:0.185542:136:154:GLOD4                                              .:.:.:.:.:.:.:.  -0.0156192:0.043738:0.721241:-570682:0.185542:136:154:VPS53     0.0359808:0.0739761:0.62702:-581377:0.185542:136:154:TLCD3A                             .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=TLCD3A     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.0280081:0.0528594:0.596568:-581377:0.185542:136:154:TLCD3A     0.00640265:0.061218:0.916767:-828741:0.185542:136:154:NXN                                               .:.:.:.:.:.:.:.  -0.0795696:0.0542971:0.143759:-631417:0.185542:136:154:MRM3     0.0459165:0.0638787:0.472773:-632355:0.185542:136:154:GLOD4                             .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=MRM3       STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   -0.077166:0.0560571:0.16959:-631417:0.185542:136:154:MRM3        -0.0264652:0.0814339:0.745396:-846094:0.185542:136:154:TIMM22                                           .:.:.:.:.:.:.:.  0.00394748:0.0338465:0.907226:-632355:0.185542:136:154:GLOD4    -0.079227:0.0542963:0.145481:-828741:0.185542:136:154:NXN                               .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=GLOD4      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.0382981:0.034883:0.273055:-632355:0.185542:136:154:GLOD4       .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. 0.147031:0.0538753:0.0066943:-828741:0.185542:136:154:NXN               0.0885787:0.0674267:0.189867:-846094:0.185542:136:154:TIMM22     .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=NXN        STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.100119:0.0502687:0.0472384:-828741:0.185542:136:154:NXN        .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. -0.00336568:0.0393559:0.931901:-846094:0.185542:136:154:TIMM22          .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151035  chr17:151035_T_C        T       C       .       PASS    GENE=TIMM22     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.00525658:0.0398771:0.895208:-846094:0.185542:136:154:TIMM22    .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.                                         .:.:.:.:.:.:.:.  .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
17      151041  chr17:151041_G_A        G       A       .       PASS    GENE=DOC2B      STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.17668:0.0669117:0.00867576:-30609:0.139759:102:116:DOC2B       -0.0366692:0.0726522:0.614093:-235213:0.139759:102:116:RPH3AL                                           0.0931908:0.0673909:0.167882:-828735:0.140625:86:99:NXN  0.121447:0.0677119:0.0738034:-30609:0.139759:102:116:DOC2B     0.13931:0.0875865:0.11268:-30609:0.139759:102:116:DOC2B   -0.184022:0.0836766:0.0285633:-570676:0.139759:102:116:VPS53    0.0545293:0.0861797:0.527347:-570676:0.140097:102:116:VPS53                                     -0.0754566:0.0652846:0.248602:-372099:0.139759:102:116:AC015853.3
17      151041  chr17:151041_G_A        G       A       .       PASS    GENE=RPH3AL     STAT:SE:P:TSS_D:AF:MA_SAMPLES:MA_COUNT:GENE.1                                   0.0134291:0.0780788:0.863548:-235213:0.139759:102:116:RPH3AL     -0.0111963:0.0889338:0.899893:-259284:0.139759:102:116:C17orf97                                         .:.:.:.:.:.:.:.  0.00734513:0.0826317:0.929224:-235213:0.139759:102:116:RPH3AL   -0.00278597:0.0647536:0.965709:-235213:0.139759:102:116:RPH3AL                          0.214712:0.0992383:0.0312188:-632349:0.139759:102:116:GLOD4      0.0533122:0.0946385:0.573602:-632349:0.140097:102:116:GLOD4                                             0.0813417:0.0725976:0.263346:-570676:0.139759:102:116:VPS53

[marcora]

The resulting file would not be a valid VCF file since the same variant would be present in multiple rows. INFO field is for variant-level information that does not change across samples/traits/genes, while sample/trait/gene columns are for information (like genotype or association statistics) that vary by sample/trait/gene.