Variant report

Variant	rs6905658
Chromosome Location	chr6:56741321-56741322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11968575	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs11970648	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13190784	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191084	0.89[EUR][1000 genomes]
rs13191826	0.87[ASN][1000 genomes]
rs13195825	0.98[EUR][1000 genomes]
rs13198597	0.80[CEU][hapmap]
rs13199024	0.98[EUR][1000 genomes]
rs13199233	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13200166	0.88[MEX][hapmap]
rs13200868	0.87[ASN][1000 genomes]
rs13203600	0.98[EUR][1000 genomes]
rs13205022	0.99[EUR][1000 genomes]
rs13207768	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs13209099	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13215883	0.80[CEU][hapmap]
rs13216793	0.99[EUR][1000 genomes]
rs13218913	0.89[MEX][hapmap]
rs16888171	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs16888186	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs16888189	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs16888192	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs17684802	0.89[MEX][hapmap]
rs17684878	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs17685045	0.98[EUR][1000 genomes]
rs17752106	0.81[CEU][hapmap]
rs1870638	0.93[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs1903332	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs3002010	1.00[CHB][hapmap]
rs3002011	1.00[CHB][hapmap]
rs34966024	0.87[ASN][1000 genomes]
rs35440408	0.87[ASN][1000 genomes]
rs35609883	0.87[ASN][1000 genomes]
rs35886823	0.87[ASN][1000 genomes]
rs4299824	0.89[MEX][hapmap]
rs4415160	0.89[MEX][hapmap]
rs4443500	0.89[EUR][1000 genomes]
rs58980183	0.87[ASN][1000 genomes]
rs60163288	0.87[ASN][1000 genomes]
rs60563401	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61601344	0.87[ASN][1000 genomes]
rs67063738	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6904535	0.87[ASN][1000 genomes]
rs6910414	0.87[ASN][1000 genomes]
rs6911654	0.89[EUR][1000 genomes]
rs6918949	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs6925518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926742	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934714	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs71564864	0.98[EUR][1000 genomes]
rs73457800	0.84[EUR][1000 genomes]
rs7744240	0.93[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs7744799	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs7758867	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs7761501	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs7761729	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs9464401	0.89[EUR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv508408	chr6:56735681-56773285	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6905658	BEND6	cis	parietal	SCAN
rs6905658	BEND6	cis	cerebellum	SCAN
rs6905658	DST	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56734200-56755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:56734600-56750200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:56734600-56755400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:56734800-56754200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:56734800-56754400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:56736400-56755800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:56738200-56743000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:56740400-56741400	Enhancers	Fetal Intestine Large	intestine
9	chr6:56740400-56741600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:56740400-56741600	Flanking Active TSS	A549	lung
11	chr6:56740400-56742000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:56740400-56742000	Genic enhancers	NHDF-Ad	bronchial
13	chr6:56740600-56741400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:56740800-56741600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:56740800-56742000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:56740800-56742000	Enhancers	Osteobl	bone
17	chr6:56741000-56741600	Genic enhancers	NHLF	lung
18	chr6:56741000-56741800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:56741200-56741600	Enhancers	HepG2	liver
20	chr6:56741200-56754600	Weak transcription	Muscle Satellite Cultured Cells	--

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