Variant report

Variant	rs9352829
Chromosome Location	chr6:81063877-81063878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:81063868-81064049	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000272129	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1040596	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs1042367	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs1042368	0.89[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.82[ASN][1000 genomes]
rs10864	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs1159506	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs11961331	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966170	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320614	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320615	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320616	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15062	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs1541210	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs2223876	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs2322757	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs2322758	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs2322759	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs2322761	0.82[ASN][1000 genomes]
rs2322762	0.84[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2322763	0.82[ASN][1000 genomes]
rs2874849	0.89[CEU][hapmap]
rs2874851	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs34758321	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792994	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs3805848	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[ASN][1000 genomes]
rs3805851	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs3805852	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs4134487	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4502885	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[ASN][1000 genomes]
rs4706114	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs4706115	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs5003782	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs58780569	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59904615	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454152	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs6921240	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921246	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921321	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723587	0.80[ASN][1000 genomes]
rs723588	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73467561	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467566	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467567	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467571	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467576	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740932	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs7740958	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.81[ASN][1000 genomes]
rs7745921	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758761	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs7759304	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs7762655	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs7766087	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766633	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926732	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs926733	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs9341812	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343983	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9350852	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9350853	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352819	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs9352820	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352821	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352823	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352824	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352825	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352827	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359414	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361602	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs9361603	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361604	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9361605	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9361607	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986438	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9352829	RP11-250B2.6	cis	lung	GTEx
rs9352829	PGM3	cis	parietal	SCAN
rs9352829	BCKDHB	Cis_1M	lymphoblastoid	RTeQTL
rs9352829	DNAJC15	trans	parietal	SCAN
rs9352829	BCKDHB	cis	Thyroid	GTEx

Chromatin state (count:17 , 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	chr6:81048200-81066800	Weak transcription	Pancreas	Pancrea
4	chr6:81048400-81064200	Weak transcription	Liver	Liver
5	chr6:81050400-81071200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:81053600-81073800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:81057200-81067200	Weak transcription	Fetal Lung	lung
8	chr6:81058400-81067000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:81058400-81071400	Weak transcription	Aorta	Aorta
10	chr6:81058400-81075800	Weak transcription	Psoas Muscle	Psoas
11	chr6:81059200-81069000	Weak transcription	Fetal Stomach	stomach
12	chr6:81060600-81069000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:81062600-81067000	Weak transcription	NHDF-Ad	bronchial
14	chr6:81063000-81070400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:81063800-81066800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:81063800-81067000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:81063800-81068800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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