Table I.
Genes and classes of genes that contain clustered SNPs that provide nominally-significant abuser vs control differences in both European-American and African-American NIDA (N) samples [68]. The numbers of SNPs within each gene (exons +/− 100kb flank) that display nominally-significant differences in comparisons between N: polysubstance abusers and control individuals in both replicate NIDA samples [51] C: alcohol dependent vs control COGA samples [68, 77], J: methamphetamine dependent vs control samples from JGIDA (Drgon et al, manuscript in preparation), T: methamphetamine dependent vs control samples from Taiwan (Uhl et al, manuscript in preparation) and B: nicotine dependent smokers vs nondependent smokers from Australia and the US [87]. Genes are grouped by the class of the function to which they contribute: “CAM” cell adhesion, “CHA” channels, “DIS” disease associated, “ENZ” enzymes, “OTHER” other functions, “PROT” protein processing, “REC” receptors (combining single TM, seven TM and ligand-gated channel families), “STR” structural, “TF” transcriptional regulation, “TRANSP” transporters, and unknown functions.
Chromosome number and initial chromosomal position for the cluster (bp, NCBI Mapviewer Build 36.1) are listed. Several genes are identified by the same clusters of positive SNPs.
| Nominally-positive SNPS | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene [51] | Class | gene description | ch | bp | N | C | J | T | B |
| CSMD2 | CAM | CUB and Sushi multiple domains 2 | 1 | 33752196 | 8 | 27 | 6 | 11 | |
| LRP1B | CAM | low density lipoprotein-related protein 1B | 2 | 140705466 | 15 | 73 | 38 | 16 | 4 |
| CNTN6 | CAM | contactin 6 | 3 | 1109629 | 4 | 17 | 6 | 13 | 6 |
| CNTN4 | CAM | contactin 4 | 3 | 2117247 | 6 | 32 | 14 | 10 | |
| LRRN1 | CAM | leucine rich repeat neuronal 1 | 3 | 3816554 | 3 | 13 | 9 | 1 | |
| LPHN3 | CAM | latrophilin 3 | 4 | 62045434 | 3 | 7 | 9 | 3 | |
| CTNND2 | CAM | catenin delta 2 | 5 | 11024952 | 5 | 53 | 17 | 8 | |
| TRIO | CAM | triple functional domain/PTPRF interacting | 5 | 14196829 | 6 | 11 | 3 | 7 | |
| BAI3 | CAM | brain-specific angiogenesis inhibitor 3 | 6 | 69404158 | 6 | 24 | 7 | 1 | |
| SEMA3C | CAM | semaphorin 3C | 7 | 80209790 | 4 | 10 | 7 | 0 | |
| CSMD1 | CAM | CUB and Sushi multiple domains 1 | 8 | 2782789 | 19 | 115 | 48 | 36 | 12 |
| SGCZ | CAM | sarcoglycan zeta | 8 | 13991744 | 11 | 61 | 35 | 17 | |
| PTPRD | CAM | receptor type protein tyrosine phosphatase D | 9 | 8307268 | 4 | 40 | 13 | 7 | 2 |
| LRRN6C | CAM | leucine rich repeat neuronal 6C | 9 | 27938528 | 10 | 44 | 23 | 21 | 18 |
| CTNNA3 | CAM | catenin alpha 3 | 10 | 67349937 | 11 | 33 | 18 | 7 | 21 |
| CNTN5 | CAM | contactin 5 | 11 | 98397081 | 7 | 42 | 18 | 9 | 7 |
| ANKS1B | CAM | ankyrin repeat and sterile alpha motif domain containing 1B | 12 | 97653202 | 5 | 17 | 13 | 5 | |
| POSTN | CAM | periostin | 13 | 37034779 | 6 | 10 | 11 | 4 | |
| CDH13 | CAM | cadherin 13 | 16 | 81218079 | 9 | 107 | 41 | 39 | 2 |
| DSCAM | CAM | Down syndrome cell adhesion molecule | 21 | 40306213 | 4 | 24 | 31 | 16 | |
| GJA5 | CHA | connexin 40 | 1 | 145695517 | 3 | 9 | 4 | 0 | |
| KCNQ3 | CHA | KQT-like voltage-gated potassium channel member 3 | 8 | 133210438 | 6 | 16 | 7 | 4 | 2 |
| TRPC4 | CHA | transient receptor potential cation channel C,4 | 13 | 37108795 | 4 | 11 | 5 | 4 | |
| KCNH5 | CHA | voltage-gated potassium channel H 5 | 14 | 62243698 | 6 | 13 | 6 | 3 | |
| RYR3 | CHA | ryanodine receptor 3 | 15 | 31390469 | 7 | 37 | 17 | 10 | 3 |
| ALS2CR19 | DIS | amyotrophic lateral sclerosis 2 chromosome region candidate 19 | 2 | 205118761 | 4 | 25 | 11 | 8 | 3 |
| PTHB1 | DIS | parathyroid hormone-responsive B1 | 7 | 33135677 | 4 | 9 | 8 | 3 | |
| AAA1 | DIS | AAA1 protein | 7 | 34356559 | 5 | 38 | 3 | 11 | 5 |
| ATXN10 | DIS | ataxin 10 | 22 | 44446351 | 4 | 9 | 5 | 1 | |
| TTLL7 | ENZ | tubulin tyrosine ligase-like family member 7 | 1 | 84107645 | 3 | 11 | 3 | 1 | |
| ACP6 | ENZ | lysophposphatidic acid phosphatase 6 | 1 | 145585792 | 4 | 8 | 4 | 0 | 1 |
| PTGS2 | ENZ | prostaglandin-endoperoxide synthase 2 | 1 | 184907592 | 3 | 7 | 2 | 0 | |
| DAF | ENZ | decay accelerating factor for complement | 1 | 205561488 | 5 | 3 | 21 | 8 | |
| SIPA1L2 | ENZ | signal-induced proliferation-associated 1 like 2 | 1 | 230600337 | 5 | 15 | 10 | 4 | |
| CAPN13 | ENZ | calpain 13 | 2 | 30799141 | 3 | 6 | 9 | 1 | 2 |
| CPS1 | ENZ | carbamoyl-phosphate synthetase 1 | 2 | 211129583 | 3 | 11 | 5 | 1 | |
| FHIT | ENZ | fragile histidine triad gene | 3 | 59710076 | 9 | 65 | 35 | 18 | 2 |
| PDE4D | ENZ | phosphodiesterase 4D | 5 | 58302468 | 4 | 11 | 12 | 9 | |
| UST | ENZ | uronyl-2-sulfotransferase | 6 | 149110157 | 5 | 8 | 4 | 5 | 4 |
| DGKB | ENZ | diacylglycerol kinase beta | 7 | 14153770 | 6 | 29 | 9 | 3 | |
| CHN2 | ENZ | chimerin 2 | 7 | 29200646 | 7 | 25 | 8 | 7 | |
| PDE1C | ENZ | phosphodiesterase 1C | 7 | 31795772 | 3 | 8 | 7 | 0 | |
| CAMK1D | ENZ | calcium/calmodulin-dependent protein kinase ID | 10 | 12431589 | 3 | 16 | 10 | 9 | |
| PRKG1a | ENZ | cGMP-dependent protein kinase I | 10 | 52504299 | 14 | 36 | 19 | 24 | |
| HPSE2 | ENZ | heparanase 2 | 10 | 100208867 | 5 | 29 | 14 | 8 | 3 |
| PZP | ENZ | pregnancy-zone protein | 12 | 9192703 | 3 | 3 | 6 | 2 | |
| SERPINA1 | ENZ | serpin peptidase inhibitor A 1 | 14 | 93914451 | 4 | 4 | 4 | 1 | |
| SERPINA2 | ENZ | serpin peptidase inhibitor A 2 | 14 | 93900404 | 4 | 3 | 4 | 1 | |
| USP31 | ENZ | ubiquitin specific peptidase 31 | 16 | 22986868 | 3 | 6 | 3 | 3 | |
| CHST9 | ENZ | carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9 | 18 | 22749593 | 3 | 9 | 6 | 1 | |
| RBMS3 | OTHER | RNA binding motif, single stranded interacting protein | 3 | 29297947 | 5 | 21 | 11 | 2 | 8 |
| RPA3 | OTHER | replication protein A3 | 7 | 7643100 | 5 | 11 | 2 | 0 | |
| HHLA1 | OTHER | HERV-H LTR-associating 1 | 8 | 133145212 | 4 | 7 | 5 | 0 | |
| RAB2-like | OTHER | FLJ45872 protein | 8 | 138890869 | 3 | 19 | 10 | 5 | |
| FGF14 | OTHER | fibroblast growth factor 14 | 13 | 101173036 | 4 | 29 | 9 | 6 | 5 |
| A2BP1 | OTHER | ataxin 2-binding protein 1 | 16 | 6009133 | 11 | 102 | 37 | 21 | 13 |
| OSBPL1A | OTHER | oxysterol binding protein-like 1A | 18 | 19996007 | 4 | 10 | 4 | 1 | |
| EPB41L2 | PROT | erythrocyte membrane protein band 4.1-like 2 | 6 | 131202180 | 3 | 17 | 2 | 1 | |
| ELMO1 | PROT | engulfment and cell motility 1 | 7 | 36860486 | 5 | 24 | 8 | 12 | |
| SORCS1 | PROT | sortilin-related VPS10 domain containing receptor 1 | 10 | 108323411 | 4 | 17 | 10 | 7 | 3 |
| MICALCL | PROT | MICAL C-terminal like | 11 | 12271946 | 3 | 10 | 9 | 3 | |
| MCTP2 | PROT | multiple C2 domains, transmembrane 2 | 15 | 92642499 | 3 | 5 | 5 | 4 | |
| IMPACT | PROT | Impact homolog | 18 | 20260680 | 4 | 8 | 3 | 1 | |
| DOK6 | PROT | docking protein 6 | 18 | 65219271 | 6 | 15 | 1 | 2 | |
| NAPB | PROT | neuritis with brachial prediliction | 20 | 23303165 | 3 | 7 | 1 | 7 | |
| CRIM1 | REC | cysteine rich transmembrane BMP regulator 1 | 2 | 36436901 | 5 | 16 | 13 | 12 | |
| GPR39 | REC | G protein-coupled receptor 39 | 2 | 132891086 | 4 | 8 | 3 | 4 | |
| bFGFR-like | REC | hypothetical protein FLJ32955 | 2 | 150332266 | 3 | 10 | 5 | 2 | |
| GRM7 | REC | glutamate receptor, metabotropic 7 | 3 | 6877927 | 5 | 59 | 24 | 14 | |
| GABRG1 | REC | GABA A receptor gamma 1 | 4 | 45732543 | 3 | 7 | 2 | 0 | |
| NPSR1 | REC | neuropeptide S receptor 1 | 7 | 34664422 | 5 | 32 | 3 | 8 | 3 |
| HRH4 | REC | histamine receptor H4 | 18 | 20294591 | 3 | 7 | 1 | 0 | |
| ACTN2 | STR | alpha 2 actinin | 1 | 234916422 | 3 | 5 | 3 | 2 | |
| OC90 | STR | similar to Otoconin 90 precursor | 8 | 133105910 | 4 | 5 | 5 | 0 | |
| AKAP13 | STR | A kinase anchor protein 13 | 15 | 83724875 | 3 | 12 | 7 | 4 | |
| FERD3L | TF | Fer3-like | 7 | 19150930 | 3 | 2 | 2 | 0 | |
| TWIST1 | TF | twist homolog 1 | 7 | 19121616 | 3 | 2 | 2 | 0 | |
| CNDB1 | TF | cyclic nucleotide binding domain containing 1 | 8 | 87947789 | 5 | 4 | 5 | 0 | |
| NFIB | TF | nuclear factor I/B | 9 | 14071847 | 3 | 13 | 3 | 3 | |
| E2F7 | TF | E2F transcription factor 7 | 12 | 75939159 | 4 | 2 | 2 | 1 | |
| NPAS3 | TF | neuronal PAS domain protein 3 | 14 | 32478200 | 8 | 43 | 24 | 5 | |
| ZNF407 | TF | zinc finger protein 407 | 18 | 70474282 | 5 | 20 | 2 | 0 | |
| NRIP1 | TF | nuclear receptor interacting protein 1 | 21 | 15255427 | 4 | 5 | 2 | 1 | |
| SLC9A9 | TRANSP | sodium/hydrogen exchanger 9 | 3 | 144466754 | 6 | 17 | 6 | 5 | 5 |
| XKR4 | TRANSP | XK family 4 | 8 | 56177571 | 8 | 20 | 4 | 11 | |
| ABCC4 | TRANSP | ATP-binding cassette C 4 | 13 | 94470090 | 3 | 11 | 10 | 4 | |
| CCDC93 | unknown | coiled-coil domain containing 93 | 2 | 118389617 | 5 | 6 | 1 | 1 | |
| KIAA1679 | unknown | KIAA1679 protein | 2 | 137464932 | 3 | 23 | 17 | 4 | |
| FLJ37543 | unknown | hypothetical protein FLJ37543 | 5 | 60969393 | 3 | 4 | 7 | 4 | |
| FLJ20323 | unknown | hypothetical protein FLJ20323 | 7 | 7573149 | 5 | 7 | 4 | 0 | |
| KIAA0143 | unknown | KIAA0143 protein | 8 | 133021330 | 3 | 5 | 8 | 0 | |
| KIAA1713 | unknown | KIAA1713 | 18 | 29412569 | 5 | 7 | 9 | 1 | |
| CCDC102B | unknown | coiled-coil domain containing 102B | 18 | 64655575 | 3 | 11 | 5 | 0 | |