Table 3 List of Neanderthal-derived brain-related quantitative trait loci (QTL) enriched in different ethnicities in autism.
From: Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings
Locus | Rs ID | Frequency in controls | Host gene(s) | Consequence (dbSNP) | Host genes with SNPs in LD |
|---|---|---|---|---|---|
Black, Non-Hispanic (BNH) | Â | Â | Â | ||
10:132208002:G>A | rs79220014 | Rare | STK32C | STK32C : Non Coding Transcript Variant | DPYSL4 JAKMIP3 |
17:14076741:A>T | rs2230351 | Rare | COX10 | COX10 : Missense Variant (T>S) | CDRT15 |
5:34908772:T>C | rs1805327 | Rare | RAD1 | RAD1 : Missense Variant (E>G)TTC23L : Intron Variant | RAI14 |
11:12008896:C>G | rs28411401 | Rare | DKK3 | DKK3 : Intron Variant | MICAL2 |
6:44304547:G>C | rs74950428 | Rare | AARS2; POLR1C | POLR1C : Intron VariantAARS2 : Intron Variant | NA |
6:44304587:C>A | rs74964556 | Rare | AARS2; POLR1C | POLR1C : Intron VariantAARS2 : Intron Variant | NA |
White, Hispanic (WHS) | |||||
12:47784123:C>T | rs7306788 | Common | HDAC7 | HDAC7 : Synonymous Variant | AMIGO2 ENDOU PCED1B TMEM106C RAPGEF3 SLC48A1 |
15:74195628:A>T | rs971756 | Common | STRA6 | STRA6 : Missense Variant (L>M) | MPI SCAMP2 SEMA7A UBL7 |
15:74195505:G>A | rs971757 | Common | STRA6 | STRA6 : Intron Variant | MPI SCAMP2 SEMA7A UBL7 |
20:3191844:A>G | rs73075075 | Common | DDRGK1 | DDRGK1 : Intron Variant | DNAAF9 ITPA SLC4A11 |
17:78222788:G>A | rs17882271 | Common | BIRC5 | BIRC5 : Intron Variant | TMEM235 |
3:8733903:C>T | rs1974763 | Common | CAV3 | CAV3 : Synonymous Variant | NA |
20:63564680:C>T | rs3810487 | Common | HELZ2 | HELZ2 : Missense Variant (R>K) | GMEB2 LIME1 ARFRP1 RTEL1 ZGPAT SLC2A4RG STMN3 |
15:83942878:G>A | rs12901723 | Common | ADAMTSL3 | ADAMTSL3 : Intron Variant | ALPK3 GOLGA6L4 HOMER2 NMB WDR73 |
10:132208002:G>A | rs79220014 | Common | STK32C | STK32C : Non Coding Transcript Variant | DPYSL4 JAKMIP3 |
21:42575315:A>C | rs112406029 | Common | SLC37A1 | SLC37A1 : Intron VariantLOC101928212 : 2KB Upstream Variant | PDE9A RSPH1 SLC37A1 |
11:11956026:T>C | rs2307073 | Common | USP47 | USP47 : Synonymous Variant | DKK3 |
6:44147432:G>A | rs4714759 | Common | TMEM63B | TMEM63B : Missense Variant (V>M)POLR1C : Intron Variant | MRPL14 |
6:44151939:A>G | rs3734697 | Common | TMEM63B | TMEM63B : Synonymous VariantPOLR1C : Intron Variant | MRPL14 |
6:44149927:C>T | rs4714762 | Common | TMEM63B | TMEM63B : Synonymous VariantPOLR1C : Intron Variant | MRPL14 |
6:41734881:C>A | rs4487571 | Rare | TFEB | TFEB : Intron VariantMIR10398 : 2KB Upstream Variant | NA |
1:85124159:A>G | rs17121745 | Common | DNAI3 | DNAI3 : Missense Variant (T>A) | NA |
1:84483058:T>C | rs147475122 | Common | RPF1 | RPF1 : Intron Variant | NA |
19:7731701:T>G | rs117034642 | Common | CLEC4G | CLEC4G : Synonymous Variant | CD209 EVI5L CLEC4M TRAPPC5 |
White, Non-Hispanic (WNH) | |||||
21:42575315:A>C | rs112406029 | Common | SLC37A1 | SLC37A1 : Intron Variant LOC101928212 : 2KB Upstream Variant | CBS PDE9A RSPH1 |
