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Genomics Inform > Volume 19(1); 2021 > Article |
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Tag SNP | rsID | SNP (P) | Trait | Journal | cRE coordinates | Cell type specificity (FDR) | Cell type |
---|---|---|---|---|---|---|---|
chr10.101946033 | rs28372851 | 5.00.E-07 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr10:101951673‒101953324 | 1.04.E-02 | Myeloid |
chr10:102012793‒102017699 | 1.20.E-04 | Myeloid | |||||
chr10:102049789‒102052812 | 8.65.E-06 | Myeloid | |||||
chr10.102048979 | rs12765052 | 1.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr10:101923384‒101944862 | 3.86.E-02 | Myeloid |
chr10:101951673‒101953324 | 1.04.E-02 | Myeloid | |||||
chr10:102012793‒102017699 | 1.20.E-04 | Myeloid | |||||
chr10:102049789‒102052812 | 8.65.E-06 | Myeloid | |||||
chr10.4961021 | rs4453114 | 2.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr10:5003981‒5007221 | 1.96.E-02 | Epithelial |
chr11.125510257 | rs113301858 | 7.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr11:125543549‒125544766 | 1.41.E-03 | Endothelial |
chr1.160210727 | rs2369473 | 7.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr1:160315750‒160319868 | 3.07.E-02 | Myeloid |
chr11.94284529 | rs12279741 | 8.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr11:94279690‒94284377 | 8.37.E-04 | Myeloid |
chr12.9058562 | rs1073160 | 3.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr12:9052330‒9056220 | 4.30.E-02 | Myeloid |
chr15.58418128 | rs2704201 | 4.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr15:58434184‒58441657 | 2.98.E-06 | Myeloid |
chr21.40173528 | rs1209950 | 3.00.E-07 | Non‒small cell lung cancer (survival) | J Thorac Oncol (2010) [24] | chr21:40169204‒40174398 | 4.52.E-02 | Cancer |
chr2.152481712 | rs10174077 | 1.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr2:152474585‒152476605 | 2.78.E-06 | Endothelial |
chr2.17784157 | rs13031455 | 2.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr2:17801191‒17803176 | 1.15.E-06 | Epithelial |
chr2.225263527 | rs6714462 | 8.00.E-06 | Familial squamous cell lung carcinoma | Carcinogenesis (2018) [25] | chr2:225270125‒225272718 | 1.63.E-02 | Endothelial |
chr2.233426526 | rs1656402 | 8.00.E-08 | Non‒small cell lung cancer (survival) | J Thorac Oncol (2010) [24] | chr2:233453904‒233458464 | 4.15.E-03 | Epithelial |
chr2.65832377 | rs840781 | 8.00.E-07 | Familial squamous cell lung carcinoma | Carcinogenesis (2018) [25] | chr2:65832165‒65835046 | 1.09.E-03 | B cell |
chr3.194858374 | rs2131877 | 2.00.E-08 | Non‒small cell lung cancer | Hum Mol Genet (2010) | chr3:194848773‒194855042 | 7.36.E-03 | B cell |
chr5.72305846 | rs258892 | 5.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr5:72083963‒72085536 | 1.41.E-03 | Epithelial |
chr5:72166471‒72170755 | 2.59.E-03 | Endothelial | |||||
chr5.82418056 | rs28745309 | 5.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr5:82420842‒82421162 | 4.56.E-02 | Cancer |
chr6.10415006 | rs654351 | 2.00.E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr6:10399644‒10415402 | 1.50.E-02 | Epithelial |
chr6.26328353 | rs34107459 | 1.00.E-10 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr6:26327078‒26331665 | 1.11.E-02 | Cancer |
chr6.26403036 | rs12200782 | 1.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr6:26393324‒26393714 | 3.84.E-02 | Myeloid |
chr6.26581258 | rs141670911 | 1.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr6:26393324‒26393714 | 3.84.E-02 | Myeloid |
chr6:26462575‒26465582 | 3.46.E-02 | Epithelial | |||||
chr6.26651053 | rs13201782 | 2.00.E-08 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr6:26462575‒26465582 | 3.46.E-02 | Epithelial |
chr6.26686131 | rs10456332 | 7.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr6:26462575‒26465582 | 3.46.E-02 | Epithelial |
chr6:26757238‒26758412 | 3.93.E-04 | Cancer | |||||
chr6:27144603‒27146930 | 3.24.E-02 | Cancer | |||||
chr6.30882415 | rs114274879 | 3.00.E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr6:30802423‒30803200 | 9.81.E-04 | T cell |
chr6:30848819‒30857882 | 4.56.E-02 | Epithelial | |||||
chr6:30889573‒30895783 | 2.35.E-03 | Epithelial | |||||
chr6.32591476 | rs112037939 | 2.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr6:32599939‒32607692 | 6.99.E-04 | B cell |
chr6.32605884 | rs74942078 | 3.00.E-17 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | chr6:32568908‒32579990 | 2.98.E-02 | B cell |
chr6:32599939‒32607692 | 6.99.E-04 | B cell | |||||
chr6:32652218‒32660026 | 2.53.E-03 | B cell | |||||
chr6.34923864 | rs847845 | 6.00.E-06 | Non-small cell lung cancer | Carcinogenesis (2013) [27] | chr6:34938580‒34938872 | 5.21.E-03 | Fibroblast |
chr6.7770511 | rs140013431 | 1.00.E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | chr6:7770218‒7770887 | 4.90.E-02 | Endothelial |
Gene ID | Ensemble ID | cRE coordinates | Cell type | Cell type specificity (FDR) | Tag SNP | rsID | SNP (P) | Trait | Journal |
Z-transformed gene expression |
|||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Myeloid | B cell | T cell | Epithelial | Fibroblast | Endothelial | ||||||||||
PSORS1C2 | ENSG00000204538.3 | chr6:30848819‒30857882 | Epithelial | 3.16.E-02 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.447 | -0.447 | -0.447 | 2.236 | -0.447 | -0.447 |
SFTA2 | ENSG00000196260.3 | chr6:30848819‒30857882 | Epithelial | 3.16.E-02 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.412 | -0.457 | -0.448 | 2.236 | -0.465 | -0.454 |
DPCR1 | ENSG00000168631.7 | chr6:30848819‒30857882 | Epithelial | 3.16.E-02 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.442 | -0.451 | -0.461 | 2.236 | -0.408 | -0.474 |
MUC21 | ENSG00000204544.5 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.399 | -0.469 | -0.431 | 2.235 | -0.462 | -0.476 |
DDR1 | ENSG00000204580.7 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.467 | -0.456 | -0.509 | 2.232 | -0.323 | -0.477 |
MUC22 | ENSG00000261272.1 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.442 | -0.497 | -0.299 | 2.231 | -0.497 | -0.497 |
DGKD | ENSG00000077044.5 | chr2:233453904‒233458464 | Epithelial | 1.07.E-03 | chr2.233426526 | rs1656402 | 8.00E-08 | Non‒smallcelllungcancer(survival) | J Thorac Oncol (2010) [24] | -0.486 | -0.105 | -0.336 | 2.197 | -0.681 | -0.589 |
POU5F1 | ENSG00000204531.11 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.696 | -0.595 | -0.630 | 2.066 | -0.565 | 0.419 |
CCHCR1 | ENSG00000204536.9 | chr6:30848819‒30857882 | Epithelial | 3.16.E-02 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.685 | -0.730 | -0.680 | 2.062 | 0.392 | -0.358 |
PSORS1C1 | ENSG00000204540.6 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.737 | -0.777 | -0.783 | 2.052 | 0.090 | 0.155 |
VARS2 | ENSG00000137411.12 | chr6:30848819‒30857882 | Epithelial | 3.16.E-02 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.370 | -0.835 | -1.131 | 1.951 | 0.240 | 0.144 |
TIGD1 | ENSG00000221944.3 | chr2:233453904‒233458464 | Epithelial | 1.07.E-03 | chr2.233426526 | rs1656402 | 8.00E-08 | Non‒small cell lung cancer (survival) | J Thorac Oncol (2010) [24] | -1.161 | -0.796 | 0.255 | 1.939 | -0.406 | 0.169 |
KLHDC10 | ENSG00000128607.9 | chr7:130666628‒130685063 | Epithelial | 2.00.E-02 | chr7.130668618 | rs6957511 | 1.00E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.355 | -1.310 | -1.074 | 1.491 | 0.584 | 0.665 |
CHRND | ENSG00000135902.5 | chr2:233453904‒233458464 | Epithelial | 1.07.E-03 | chr2.233426526 | rs1656402 | 8.00E-08 | Non‒smallcelllungcancer(survival) | J Thorac Oncol (2010) [24] | 0.534 | -0.964 | 0.910 | 1.449 | -0.964 | -0.964 |
C6orf15 | ENSG00000204542.2 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.770 | -0.770 | -0.505 | 1.368 | -0.770 | 1.352 |
PRR3 | ENSG00000204576.7 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.377 | -1.297 | -0.856 | 1.269 | 1.131 | -0.090 |
GIGYF2 | ENSG00000204120.10 | chr2:233453904‒233458464 | Epithelial | 1.07.E-03 | chr2.233426526 | rs1656402 | 8.00E-08 | Non‒small cell lung cancer (survival) | J Thorac Oncol (2010) [24] | -0.487 | -1.368 | -1.013 | 1.242 | 0.815 | 0.811 |
ZNF322 | ENSG00000181315.6 | chr6:27094480‒27096156 | Epithelial | 2.58.E-02 | chr6.26686131 | rs10456332 | 7.00E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | -0.550 | -1.106 | -1.227 | 1.209 | 1.067 | 0.606 |
MDC1 | ENSG00000137337.10 | chr6:30889573‒30895783 | Epithelial | 1.61.E-05 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -0.883 | -1.281 | -0.782 | 1.178 | 0.974 | 0.794 |
HYLS1 | ENSG00000198331.6 | chr11:125543549‒125544766 | Endothelial | 9.66.E-04 | chr11.125510257 | rs113301858 | 7.00E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | -1.371 | -0.807 | 0.263 | -0.207 | 0.318 | 1.804 |
IL1R1 | ENSG00000115594.7 | chr2:102854553‒102858050 | Fibroblast | 3.09.E-02 | chr2.102857739 | rs185815317 | 1.00E-06 | Familialsquamouscelllungcarcinoma | Carcinogenesis (2018) [25] | -0.792 | -1.055 | -1.004 | 0.611 | 1.550 | 0.689 |
BLOC1S2 | ENSG00000196072.7 | chr10:102012793‒102017699 | Myeloid | 1.79.E-04 | chr10.102048979 | rs12765052 | 1.00E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | 2.161 | -0.253 | -0.008 | -0.780 | -0.438 | -0.682 |
CLEC4E | ENSG00000166523.3 | chr12:9052330‒9056220 | Myeloid | 3.18.E-02 | chr12.9058562 | rs1073160 | 3.00E-06 | Small cell lung carcinoma | Nat Genet (2017) [23] | 1.837 | -0.689 | -0.678 | -0.657 | -0.695 | 0.882 |
CD84 | ENSG00000066294.10 | chr1:160315750‒160319868 | Myeloid | 2.06.E-02 | chr1.160210727 | rs2369473 | 7.00E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | 1.760 | -0.255 | 0.928 | -0.812 | -0.814 | -0.808 |
CHUK | ENSG00000213341.6 | chr10:101951673‒101953324 | Myeloid | 1.17.E-02 | chr10.102048979 | rs12765052 | 1.00E-06 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | 1.459 | -1.436 | -0.536 | 1.058 | -0.629 | 0.084 |
PPP1R18 | ENSG00000146112.7 | chr6:30802423‒30803200 | Tcell | 2.70.E-04 | chr6.30882415 | rs114274879 | 3.00E-16 | Squamous cell lung carcinoma | Nat Genet (2017) [23] | 0.965 | -0.295 | 1.539 | -1.526 | -0.501 | -0.183 |
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