Variant report

Variant	rs9352820
Chromosome Location	chr6:81057451-81057452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1040592	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1040594	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1040595	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1040596	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1042367	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs1042368	0.90[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10864	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1157978	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1157979	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1159505	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1159506	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11961331	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966170	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320614	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320615	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320616	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474790	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs15062	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1541208	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1541209	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1541210	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1541211	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1546928	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1546930	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1883974	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1883975	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1883976	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1988589	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2143885	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2143886	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2179839	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2179840	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2179841	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2179843	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2207142	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2207143	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2223874	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2223876	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322749	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322750	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322751	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322752	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322754	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322755	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322756	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322757	0.90[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322758	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322759	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322760	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2322761	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2322762	0.85[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2322763	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2874849	0.90[CEU][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2874851	0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34758321	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792994	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3805848	0.84[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3805850	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3805851	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3805852	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3805856	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3828746	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4134487	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235812	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4502885	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4613773	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4706114	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4706115	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4706118	0.87[AFR][1000 genomes]
rs4706837	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4706838	0.89[AFR][1000 genomes]
rs4706839	0.89[AFR][1000 genomes]
rs5003782	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs58780569	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59904615	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454152	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6921240	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921246	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921321	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700491	0.86[YRI][hapmap]
rs723587	0.80[ASN][1000 genomes]
rs723588	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73467561	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467566	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467567	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467571	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467576	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740932	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7740958	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7742132	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7742563	0.84[AFR][1000 genomes]
rs7745921	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747016	0.89[YRI][hapmap]
rs7758761	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7759304	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7762655	0.90[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7766087	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766633	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767703	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs806845	0.93[YRI][hapmap]
rs806847	0.92[YRI][hapmap]
rs806848	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs926731	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs926732	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs926733	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9341812	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9350852	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9350853	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352818	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9352819	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9352821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352824	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352825	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352827	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352829	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361602	0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9361603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361604	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361605	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9361607	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9443745	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs986438	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1796319	chr6:81034505-81058025	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv463907	chr6:81047559-81075912	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv604053	chr6:81047559-81075912	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv970303	chr6:81050335-81062570	Enhancers Weak transcription	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9352820	BCKDHB	cis	Thyroid	GTEx
rs9352820	RP11-250B2.6	cis	lung	GTEx
rs9352820	BCKDHB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81029400-81079600	Weak transcription	HSMM	muscle
2	chr6:81033800-81070200	Weak transcription	Left Ventricle	heart
3	chr6:81048200-81058000	Weak transcription	Psoas Muscle	Psoas
4	chr6:81048200-81066800	Weak transcription	Pancreas	Pancrea
5	chr6:81048400-81064200	Weak transcription	Liver	Liver
6	chr6:81050400-81071200	Weak transcription	Primary T cells from cord blood	blood
7	chr6:81051600-81059200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:81053600-81073800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:81056800-81058400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:81057200-81058000	Weak transcription	Aorta	Aorta
11	chr6:81057200-81067200	Weak transcription	Fetal Lung	lung
12	chr6:81057400-81063600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links