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. 2021 Aug 13;31(2):289–299. doi: 10.1093/hmg/ddab229

Table 1.

Forty-two gene expression-trait associations for genes at genomic loci at least 500 kb away from any GWAS-identified Alzheimer’s disease risk variants

Region Gene Typea Model R  2 b Number of SNPs in model OR (95% CI) P-valuec P-value after FDRc Closest risk SNPd Distance to the risk SNP (kb)
1p36.12 HP1BP3 protein UTMOST 0.18 5 1.29 (1.13–1.47) 1.31 × 10−4 2.28 × 10−2 rs4575098 140 042
2p22.2 CEBPZOS protein LASSO 0.09 31 0.97 (0.96–0.99) 3.68 × 10−4 4.78 × 10−2 rs4663105 90 448
2q14.2 TMEM177 protein LASSO 0.03 39 0.94 (0.92–0.96) 8.10 × 10 −7 3.68 × 10−4 rs4663105 7447
2q33.2 CARF protein UTMOST 0.01 35 1.10 (1.06–1.15) 5.63 × 10−6 1.69 × 10−3 rs10933431 30 129
3q25.31 PLCH1 protein LASSO 0.02 12 0.92 (0.89–0.96) 1.44 × 10−5 3.43 × 10−3 rs184384746 97 867
4q25 FAM241A protein UTMOST 0.06 23 0.96 (0.95–0.98) 2.59 × 10 −6 8.96 × 10−4 rs6448451 102 042
LASSO 0.10 8 0.96 (0.94–0.98) 1.07 × 10−5 2.65 × 10−3 rs6448451 102 042
6p25.1 LY86 protein LASSO 0.19 14 1.02 (1.01–1.03) 3.09 × 10−4 4.10 × 10−2 rs9271192 25 923
UST protein LASSO 0.08 32 0.96 (0.95–0.98) 1.66 × 10−4 2.76 × 10−2 rs10948363 101 580
6p24.2 TMEM170B protein UTMOST 0.15 28 1.02 (1.01–1.04) 2.27 × 10−4 3.37 × 10−2 rs9271192 20 995
7p22.1 SLC29A4 protein LASSO 0.03 34 1.05 (1.02–1.07) 1.78 × 10−4 2.93 × 10−2 rs2718058 32 495
7p21.3 TMEM106B protein UTMOST 0.15 24 0.95 (0.93–0.97) 6.73 × 10−5 1.32 × 10−2 rs2718058 25 559
7q32.2 NRF1 protein UTMOST 0.02 13 1.13 (1.08–1.19) 1.19 × 10 −6 5.03 × 10−4 rs7810606 13 711
7q32.3 AC058791.1 lncRNA UTMOST 0.02 1 0.80 (0.72–0.90) 1.83 × 10−4 2.95 × 10−2 rs7810606 12 484
8q22.1 TP53INP1 protein UTMOST 0.08 8 0.94 (0.92–0.97) 2.08 × 10−4 3.23 × 10−2 rs9331896 68 471
AC087752.3 lncRNA UTMOST 0.02 11 0.83 (0.76–0.91) 5.24 × 10−5 1.05 × 10−2 rs9331896 68 495
9q21.11 LINC01506 lncRNA UTMOST 0.15 32 1.11 (1.05–1.18) 2.58 × 10−4 3.63 × 10−2 – –
10q21.2 CCDC6 protein LASSO 0.01 8 0.87 (0.82–0.92) 2.80 × 10−6 9.30 × 10−4 rs11257238 49 831
11q13.1 SNX32 protein UTMOST 0.16 15 0.98 (0.97–0.99) 8.45 × 10−6 2.28 × 10−3 rs983392 5678
LASSO 0.30 13 0.98 (0.98–0.99) 2.19 × 10−4 3.31 × 10−2 rs983392 5678
CTSW protein LASSO 0.27 26 1.02 (1.01–1.03) 7.82 × 10−6 2.17 × 10−3 rs983392 5724
UTMOST 0.32 25 1.02 (1.01–1.02) 1.07 × 10−5 2.65 × 10−3 rs983392 5724
11q24.1 GRAMD1B protein LASSO 0.08 43 0.94 (0.91–0.97) 7.60 × 10−5 1.43 × 10−2 rs11218343 1794
14q11.2 TRAV35 other LASSO 0.13 44 1.02 (1.01–1.04) 2.23 × 10−4 3.35 × 10−2 rs17125944 30 710
PRMT5 protein LASSO 0.20 36 0.98 (0.97–0.99) 3.59 × 10−4 4.71 × 10−2 rs17125944 30 002
14q24.3 RP3-414A15.2 lncRNA LASSO 0.17 40 0.97 (0.96–0.99) 3.25 × 10−5 6.95 × 10−3 rs10498633 18 930
15q21.2 RP11-120 K9.2 lncRNA LASSO 0.03 16 0.95 (0.92–0.97) 2.01 × 10−4 3.17 × 10−2 rs442495 8170
15q24.1 CYP11A1 protein LASSO 0.02 14 0.94 (0.91–0.97) 3.00 × 10−4 4.08 × 10−2 rs117618017 11 060
15q25.1 CTSH protein UTMOST 0.39 47 1.02 (1.01–1.02) 5.79 × 10−6 1.71 × 10−3 rs117618017 15 643
16p12.3 XYLT1 protein UTMOST 0.05 3 0.69 (0.56–0.84) 3.16 × 10−4 4.17 × 10−2 rs59735493 13 568
16p11.2 INO80E protein UTMOST 0.08 29 1.02 (1.01–1.03) 3.94 × 10−5 8.05 × 10−3 rs59735493 1116
LASSO 0.08 12 1.04 (1.02–1.06) 7.87 × 10−5 1.45 × 10−2 rs59735493 1116
YPEL3 protein UTMOST 0.11 14 0.98 (0.97–0.99) 7.48 × 10−5 1.43 × 10−2 rs59735493 1025
LASSO 0.10 3 0.97 (0.95–0.98) 2.10 × 10−4 3.23 × 10−2 rs59735493 1025
AC012645.1 lncRNA LASSO 0.05 8 0.95 (0.92–0.97) 8.88 × 10−5 1.60 × 10−2 rs59735493 1018
UTMOST 0.08 10 0.94 (0.91–0.97) 1.41 × 10−4 2.41 × 10−2 rs59735493 1018
AC099524.1 lncRNA UTMOST 0.15 1 1.06 (1.03–1.09) 1.33 × 10−4 2.30 × 10−2 rs59735493 50 639
17p13.3 C17orf97 protein LASSO 0.33 44 1.01 (1.01–1.02) 3.03 × 10−4 4.08 × 10−2 rs9916042 4704
17q21.31 LSM12 protein UTMOST 0.02 18 1.22 (1.10–1.36) 3.03 × 10−4 4.08 × 10−2 rs28394864 5306
17q23.3 ACE protein LASSO 0.02 11 0.95 (0.93–0.98) 2.37 × 10−4 3.48 × 10−2 rs28394864 14 104
18q12.3-q21.1 EPG5 protein UTMOST 0.07 35 1.08 (1.04–1.12) 3.71 × 10−5 7.84 × 10−3 rs76726049 12 642
19q13.31 KCNN4 protein UTMOST 0.31 18 0.98 (0.97–0.99) 1.03 × 10−4 1.84 × 10−2 rs75627662 1128
LASSO 0.24 73 0.98 (0.97–0.99) 3.05 × 10−4 4.08 × 10−2 rs75627662 1128
19q13.42 LILRA6 protein LASSO 0.09 38 0.99 (0.98–0.99) 2.54 × 10−4 3.63 × 10−2 rs3865444 2993
AC008984.7 other LASSO 0.08 7 0.95 (0.93–0.97) 2.01 × 10 −6 7.79 × 10−4 rs3865444 3085
LILRA5 protein LASSO 0.14 17 0.97 (0.95–0.98) 7.56 × 10−6 2.13 × 10−3 rs3865444 3090
UTMOST 0.13 6 0.86 (0.81–0.92) 9.32 × 10−6 2.44 × 10−3 rs3865444 3090
AC008984.2 other LASSO 0.07 23 0.96 (0.94–0.98) 2.63 × 10−5 5.97 × 10−3 rs3865444 3092
20q13.12 TOMM34 protein LASSO 0.25 51 0.98 (0.97–0.99) 2.84 × 10−4 3.91 × 10−2 rs6014724 11 410
STK4 protein LASSO 0.02 4 0.93 (0.89–0.96) 1.99 × 10−4 3.17 × 10−2 rs6014724 11 290
a

Protein: protein coding genes; lncRNA: long noncoding RNAs; other: processed transcripts, immunoglobulin genes, or T cell receptor genes.

b

R  2: prediction performance.

c

Associations with FDR-corrected P-value ≤0.05 considered significant.

d

The closest risk SNPs identified in previous GWAS or fine-mapping studies (41,70).

A full list of all risk SNPs and their distances to the genes are presented in Supplementary Material, Table S5.