Variant report

Variant	rs11229661
Chromosome Location	chr11:58613714-58613715
allele	A/T
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	CTCF	chr11:58613600-58613750	WERI-Rb-1	eye:	n/a	n/a

Variant related genes	Relation type
GLYATL2	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1014068	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10792181	0.82[AMR][1000 genomes]
rs10792183	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10792184	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10792185	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10896825	0.82[AMR][1000 genomes]
rs10896828	0.82[AMR][1000 genomes]
rs10896830	0.82[AMR][1000 genomes]
rs10896832	0.82[AMR][1000 genomes]
rs10896845	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10896847	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10896848	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10896849	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10896851	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10896852	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10896853	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10896854	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10896856	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10896857	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10896858	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10896859	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11229617	0.84[AMR][1000 genomes]
rs11229618	0.84[AMR][1000 genomes]
rs11229623	0.84[AMR][1000 genomes]
rs11229625	0.82[AMR][1000 genomes]
rs11229626	0.82[AMR][1000 genomes]
rs11229629	0.82[AMR][1000 genomes]
rs11229649	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229650	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229651	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229652	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11229653	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229655	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229656	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229657	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229658	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229662	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11535770	0.82[AMR][1000 genomes]
rs12146504	0.82[AMR][1000 genomes]
rs12146511	0.82[AMR][1000 genomes]
rs12222236	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12223073	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12224097	0.80[AMR][1000 genomes]
rs12224475	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12225778	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12226395	0.81[AMR][1000 genomes]
rs12417075	0.81[AMR][1000 genomes]
rs12419236	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12420969	0.84[AMR][1000 genomes]
rs12421060	0.81[AMR][1000 genomes]
rs1893631	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1893632	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1938707	0.81[AMR][1000 genomes]
rs1938713	0.81[AMR][1000 genomes]
rs1943254	0.82[AMR][1000 genomes]
rs1943262	0.82[AMR][1000 genomes]
rs1943263	0.81[AMR][1000 genomes]
rs1943267	0.94[AMR][1000 genomes]
rs1943268	0.94[AMR][1000 genomes]
rs1943272	0.82[AMR][1000 genomes]
rs1943276	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1943277	0.84[AMR][1000 genomes]
rs1943280	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1943281	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1943282	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1943285	0.84[AMR][1000 genomes]
rs1943305	0.84[AMR][1000 genomes]
rs1943307	0.82[AMR][1000 genomes]
rs1943308	0.82[AMR][1000 genomes]
rs1954965	0.84[AMR][1000 genomes]
rs1962553	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2097018	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2097019	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2105743	0.84[AMR][1000 genomes]
rs2156346	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2212845	0.82[AMR][1000 genomes]
rs4373954	0.81[AMR][1000 genomes]
rs4418828	0.84[AMR][1000 genomes]
rs4939222	0.82[AMR][1000 genomes]
rs4939226	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4939227	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4939228	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4939229	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4939230	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4939231	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55906811	0.83[AMR][1000 genomes]
rs56383501	0.82[AMR][1000 genomes]
rs56407726	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56699801	0.81[AMR][1000 genomes]
rs58504618	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60850183	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7104137	0.83[EUR][1000 genomes]
rs7115145	0.83[EUR][1000 genomes]
rs72913216	0.85[AFR][1000 genomes]
rs72929706	0.82[AMR][1000 genomes]
rs72929752	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72929757	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9888240	0.82[AMR][1000 genomes]
rs9943655	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9943656	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[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	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	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:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58610800-58614200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:58610800-58614600	Enhancers	Primary hematopoietic stem cells	blood
3	chr11:58613000-58618000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:58613200-58614200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:58613400-58613800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links