Table 2.
Loci identified in QT-interval GWAS or by LQTS gene neighborhood ranking. Genes within the LQTS gene neighborhood are marked in bold. Other genes that are within 150 kb, but were not in the LQTS gene neighborhood, are not bold. A negative value in the LQTS MFPT score means the gene fell outside the LQTS neighborhood. NA means the gene did not have any protein interactions and thus could not be scored. Gray rows were not found to be significant in either of the two GWAS (52, 53), but fell in intronic or coding regions of one of the 150 highest-ranked LQTS neighborhood genes and had an association strength of P < 5 × 10−6 in the QTSCD GWAS.
| SNPs (GWAS study or LQTS neighborhood ranking)* |
Genes within 150 kb of SNP (LQTS MFPT score, distance to SNP in base pairs) |
|
|---|---|---|
| Chromosome 1 | ||
| RNF207(NA, 0) | ||
| ICMT(−5.9 × 10−6, 1883) | ||
| C1orf211(NA, 18,501) | ||
| RPL22(−0.0026, 19,690) | ||
| rs846111(Both) | HES3(NA, 24,892) | |
| GPR153(NA, 28,044) | ||
| CHD5(NA, 39,186) | ||
| ACOT7(−0.00015, 44,962) | ||
| KCNAB2(0.0014, 118,846) | ||
| rs16857031(QTGEN) | NOS1AP(0.0043, 0) | |
| rs12143842(Both) | OLFML2B(NA, 40,245) | |
| rs12029454(QTGEN) | ATF6(−0.00039, 105,037) | |
| ATP1B1(−0.00020, 0) | ||
| rs10919071(QTSCD) | NME7(−0.00024, 2286) | |
| Chromosome 2 | ||
| rs13394655 (LQTS) | SLC8A1 (0.0059, 0) | |
| Chromosome 3 | ||
| SCN5A(0.082, 0) | ||
| rs11129795(QTSCD) | ENDOGL1(NA, 22,721) | |
| rs12053903(QTGEN) | ACVR2B(−0.0012, 54,529) | |
| XYLB(NA, 132,695) | ||
| SCN10A(0.00051, 145,444) | ||
| Chromosome 6 | ||
| rs11970286(QTSCD) | C6orf204(NA, 0) | |
| rs11756438(QTGEN) | SLC35F1(NA, 41,534) | |
| PLN(0.00034, 112,044) | ||
| Chromosome 7 | ||
| KCNH2(0.20, 4186) | ||
| NOS3(0.0061, 50,284) | ||
| ABP1(−0.00023, 63,782) | ||
| ATG9B(NA, 71,441) | ||
| ABCB8(−7.6 × 10−5, 87,647) | ||
| rs4725982(QTGEN) | ACCN3(0.0012, 107,742) | |
| rs2968864(QTGEN) | CDK5(0.0047, 113,036) | |
| rs2968863(QTSCD) | SLC4A2(0.00052, 118,794) | |
| TMEM176A(NA, 119,953) | ||
| TMEM176B(NA, 123,713) | ||
| FASTK(−0.00027, 135,845) | ||
| TMUB1(NA, 140,309) | ||
| AGAP3(NA, 145,091) | ||
| Chromosome 11 | ||
| KCNQ1(0.17, 0) | ||
| rs12576239(QTGEN) | TRPM5(NA, 40,527) | |
| rs2074238(QTGEN) | TSSC4(0.00027, 59,696) | |
| rs12296050(QTSCD) | CD81(−0.00024, 66,153) | |
| TSPAN32(0.00029, 145,372) | ||
| Chromosome 16 | ||
| LITAF(−0.00022, 10,430) | ||
| rs8049607(Both) | SNN(NA, 70,548) | |
| TXNDC11(−0.00043, 81,190) | ||
| LOC400499(NA, 106,141) | ||
| CNOT1(−0.00049, 0) | ||
| SETD6(NA, 13,685) | ||
| SNORA46(NA, 15,165) | ||
| rs37062(QTGEN) | NDRG4(NA, 19,714) | |
| rs7188697(QTSCD) | SNORA50(NA, 26,462) | |
| SLC38A7(NA, 78,120) | ||
| GOT2(0.00048, 118,857) | ||
| GINS3(NA, 127,189) | ||
| Chromosome 17 | ||
| LIG3(−0.00030, 0) | ||
| RAD51L3(−0.00062, 11,749) | ||
| RFFL(NA, 11,749) | ||
| rs2074518(QTGEN) | ZNF830(NA, 34,176) | |
| CCT6B(−0.00011, 35,875) | ||
| FNDC8(NA, 124,249) | ||
| NLE1(−0.00013, 133,986) | ||
| rs9910577 (LQTS) | PRKCA (0.053, 0) | |
| Chromosome 21 | ||
| KCNE1(0.11, 0) | ||
| LOC388820(NA, 25,415) | ||
| rs1805128(QTGEN) | FAM165B(−0.00014, 46,605) | |
| RCAN1(−9.3 × 10−5, 67,104) | ||
| KCNE2(0.11, 78,239) |
*
“Both” refers to the identification of the SNP in each GWAS.