Variant report

Variant	rs7959560
Chromosome Location	chr12:20657782-20657783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10770665	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10770666	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10770668	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10841554	0.84[CEU][hapmap]
rs10841556	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10841557	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10841558	0.89[ASN][1000 genomes]
rs10841560	0.82[ASN][1000 genomes]
rs10841561	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11045285	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11045299	0.82[JPT][hapmap]
rs11045301	0.81[CHB][hapmap]
rs12228896	0.81[ASN][1000 genomes]
rs12423118	0.80[ASN][1000 genomes]
rs12425566	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12813387	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12820858	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs12822341	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4304839	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[TSI][hapmap]
rs4353322	0.90[CEU][hapmap]
rs4502032	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap]
rs4561252	0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs4762969	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4762970	0.91[CEU][hapmap]
rs4762971	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs59143079	0.82[ASN][1000 genomes]
rs6487101	0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs6487105	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs7131827	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7303620	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs7308219	0.89[ASN][1000 genomes]
rs7308418	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs7316700	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7487165	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7488735	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7488869	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7965577	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7969959	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20642400-20660000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:20645600-20658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:20647000-20660600	Weak transcription	Left Ventricle	heart
4	chr12:20647200-20664000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:20648200-20660800	Weak transcription	Aorta	Aorta
6	chr12:20649600-20660600	Weak transcription	Right Ventricle	heart
7	chr12:20649600-20662000	Weak transcription	Pancreas	Pancrea
8	chr12:20652800-20660200	Weak transcription	HUVEC	blood vessel
9	chr12:20656800-20658400	Genic enhancers	Hela-S3	cervix
10	chr12:20656800-20658600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:20656800-20658600	Enhancers	Osteobl	bone
12	chr12:20656800-20658800	Enhancers	NHDF-Ad	bronchial
13	chr12:20656800-20660600	Enhancers	A549	lung
14	chr12:20657000-20658600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:20657000-20658600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:20657000-20659400	Enhancers	Colon Smooth Muscle	Colon

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