Variant report

Variant	rs4237580
Chromosome Location	chr11:108695165-108695166
allele	C/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	TCF12	chr11:108695029-108695760	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr11:108695091-108695757	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr11:108695136-108695744	SK-N-SH	brain:	n/a	chr11:108695478-108695488

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108694511..108697317-chr11:108697385..108699740,2	K562	blood:
2	chr11:108695140..108698034-chr11:108715327..108717673,2	K562	blood:

Variant related genes	Relation type
CYCSP29	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10466523	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10502106	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10749923	0.87[EUR][1000 genomes]
rs10749926	0.87[EUR][1000 genomes]
rs10749927	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10749928	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10749929	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10789675	0.88[EUR][1000 genomes]
rs10789676	0.88[EUR][1000 genomes]
rs10789677	0.88[EUR][1000 genomes]
rs10789678	0.92[EUR][1000 genomes]
rs10789680	0.94[EUR][1000 genomes]
rs10789681	0.91[EUR][1000 genomes]
rs10789682	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789683	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789685	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789688	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10789691	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10789693	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10789694	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10789696	0.83[ASN][1000 genomes]
rs10890877	0.88[EUR][1000 genomes]
rs10890879	0.88[EUR][1000 genomes]
rs10890883	0.88[EUR][1000 genomes]
rs10890888	0.88[EUR][1000 genomes]
rs10890889	0.93[EUR][1000 genomes]
rs10890893	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10890894	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10890895	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890897	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890898	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890899	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890901	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890902	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890903	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890905	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10890908	0.83[ASN][1000 genomes]
rs11212750	0.88[EUR][1000 genomes]
rs11212771	0.89[EUR][1000 genomes]
rs11212774	0.89[EUR][1000 genomes]
rs11212797	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11212802	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11212811	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11212816	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11212825	0.81[ASN][1000 genomes]
rs11530525	0.88[EUR][1000 genomes]
rs12420572	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1824664	0.88[EUR][1000 genomes]
rs1824665	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1863366	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169562	0.84[EUR][1000 genomes]
rs2306118	0.88[EUR][1000 genomes]
rs2357224	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781864	0.89[EUR][1000 genomes]
rs3781866	0.89[EUR][1000 genomes]
rs3781867	0.87[EUR][1000 genomes]
rs3902843	0.86[EUR][1000 genomes]
rs4027488	0.89[EUR][1000 genomes]
rs4497371	0.92[EUR][1000 genomes]
rs4753849	0.93[EUR][1000 genomes]
rs4753852	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4754354	0.90[EUR][1000 genomes]
rs4754357	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754358	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4754359	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4754366	0.83[ASN][1000 genomes]
rs61912810	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7103086	0.89[EUR][1000 genomes]
rs7116062	0.89[EUR][1000 genomes]
rs7940595	0.88[EUR][1000 genomes]
rs890237	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv898386	chr11:108409442-108831875	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv898388	chr11:108440814-108724639	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108675600-108709400	Weak transcription	Left Ventricle	heart
2	chr11:108675800-108700000	Weak transcription	GM12878-XiMat	blood
3	chr11:108676000-108708000	Weak transcription	Primary B cells from cord blood	blood
4	chr11:108677600-108709600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:108680400-108709400	Weak transcription	Primary T cells from cord blood	blood
6	chr11:108680600-108724400	Weak transcription	Aorta	Aorta
7	chr11:108687000-108717000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:108689800-108695400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:108692200-108709400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:108692400-108695600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr11:108694800-108695200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:108694800-108696000	Enhancers	HUVEC	blood vessel
13	chr11:108695000-108695200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:108695000-108696400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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