Variant report

Variant	rs6761276
Chromosome Location	chr2:113832312-113832313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10169599	0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[LWK][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10181720	0.91[CHB][hapmap];0.81[CHD][hapmap];0.87[LWK][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10184259	0.91[CHB][hapmap];0.92[CHD][hapmap];0.87[LWK][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10186133	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11677088	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11678375	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11682107	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11887823	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11891557	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12466799	0.91[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12468224	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12469822	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs12477866	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12477867	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12711750	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12711751	1.00[CHB][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12711752	0.83[ASW][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs13386602	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13389457	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13398125	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759676	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv874894	chr2:113830057-113832981	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv582710	chr2:113831643-113832981	Weak transcription Enhancers Active TSS	CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Protein quantitative trait loci	18464913	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6761276	ZC3H6	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113825400-113833000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:113825800-113832800	Enhancers	NHEK	skin
3	chr2:113825800-113839600	Enhancers	HMEC	breast
4	chr2:113826200-113833200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:113827400-113832400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:113827800-113832600	Weak transcription	Fetal Intestine Large	intestine
7	chr2:113829200-113832800	Enhancers	Esophagus	oesophagus
8	chr2:113830800-113833800	Enhancers	Fetal Muscle Leg	muscle
9	chr2:113831400-113834000	Weak transcription	Stomach Mucosa	stomach
10	chr2:113831600-113832600	Enhancers	Lung	lung
11	chr2:113831800-113832400	Weak transcription	Fetal Intestine Small	intestine
12	chr2:113831800-113832600	Enhancers	Gastric	stomach
13	chr2:113831800-113833000	Enhancers	Primary T cells from cord blood	blood
14	chr2:113831800-113833000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr2:113831800-113833200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:113832000-113832400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:113832000-113832800	Enhancers	Placenta	Placenta
18	chr2:113832000-113833000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:113832000-113833800	Enhancers	Fetal Thymus	thymus
20	chr2:113832200-113832800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr2:113832200-113833000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:113832200-113833000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links