Variant report

Variant	rs12222236
Chromosome Location	chr11:58598699-58598700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10896818	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs10896822	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs11229594	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs11229595	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11229597	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11229601	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs11229602	0.80[AMR][1000 genomes]
rs11229603	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs11229612	0.85[AMR][1000 genomes]
rs11229613	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11229617	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11229618	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11229620	0.80[EUR][1000 genomes]
rs11229623	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11229652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229661	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11229662	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11530801	0.83[CEU][hapmap]
rs12223073	0.93[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12226395	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12417075	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12420969	0.89[AMR][1000 genomes]
rs12421060	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17152916	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1938707	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1938713	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1938717	0.85[AMR][1000 genomes]
rs1943267	0.83[AMR][1000 genomes]
rs1943268	0.83[AMR][1000 genomes]
rs1943277	0.89[AMR][1000 genomes]
rs1943285	0.89[AMR][1000 genomes]
rs1943305	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1954965	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2105743	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2186414	0.81[YRI][hapmap]
rs35649133	0.80[AMR][1000 genomes]
rs3901271	0.81[AFR][1000 genomes]
rs3920943	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs4373954	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4418828	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55906811	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56073415	0.80[AMR][1000 genomes]
rs56699801	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60850183	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72915131	0.80[AFR][1000 genomes]
rs72927728	0.80[AMR][1000 genomes]
rs72927767	0.86[AMR][1000 genomes]
rs72929757	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7951340	0.80[AMR][1000 genomes]
rs9943655	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1048605	chr11:58534660-58672438	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1045858	chr11:58547772-58674568	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1052173	chr11:58553516-58678496	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv523481	chr11:58553771-58632368	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv525355	chr11:58553771-58632368	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv555103	chr11:58591863-58600210	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv555108	chr11:58594559-58600210	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv555115	chr11:58595363-58600210	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv1827788	chr11:58595883-58636405	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58596800-58604200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:58597800-58599000	Weak transcription	NHEK	skin
3	chr11:58597800-58599400	Weak transcription	HMEC	breast
4	chr11:58598000-58599000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:58598000-58599600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:58598600-58599400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:58598600-58599800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:58598600-58600200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:58598600-58601200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links