Variant report

Variant	rs10508696
Chromosome Location	chr10:25764571-25764572
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THNSL1-6	chr10:25764360-25764878	NONHSAT011804

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10508695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1069531	0.89[ASN][1000 genomes]
rs11014576	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12415532	0.91[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12763436	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12766947	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770449	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12770880	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12778509	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329255	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs1329256	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1329257	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1360123	0.99[ASN][1000 genomes]
rs1361634	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1410931	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1590833	0.83[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1592137	0.88[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1620326	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1773637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1928365	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2480348	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs2480349	0.99[ASN][1000 genomes]
rs2487819	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs2987832	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2987833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2987834	0.99[ASN][1000 genomes]
rs2987835	0.99[ASN][1000 genomes]
rs2987836	0.99[ASN][1000 genomes]
rs2987838	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2987839	0.99[ASN][1000 genomes]
rs2987840	0.82[ASN][1000 genomes]
rs3005181	0.82[ASN][1000 genomes]
rs3005182	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs3005189	0.99[ASN][1000 genomes]
rs3005191	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3005193	0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3123901	0.82[ASN][1000 genomes]
rs34535236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36146927	0.95[ASN][1000 genomes]
rs4545439	0.83[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs57048226	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66516873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67290477	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67616835	1.00[ASN][1000 genomes]
rs702980	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7075106	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7084979	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085111	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086959	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7089568	0.97[ASN][1000 genomes]
rs824588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs824607	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs824608	0.99[ASN][1000 genomes]
rs824609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs824610	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349863	chr10:25614571-25946379	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10508696	GPR158	cis	cerebellum	SCAN
rs10508696	BAMBI	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25756800-25775000	Weak transcription	K562	blood
2	chr10:25757200-25769600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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