Variant report

Variant	rs7965577
Chromosome Location	chr12:20664177-20664178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10770665	0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10770668	0.91[CHB][hapmap]
rs10841556	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10841557	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10841558	0.87[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841560	0.90[ASN][1000 genomes]
rs10841561	0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11045285	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11045299	0.82[CHB][hapmap]
rs11045301	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12228896	0.83[ASN][1000 genomes]
rs12423118	0.86[ASN][1000 genomes]
rs12425566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813387	0.87[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12820858	0.82[JPT][hapmap]
rs12822341	0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2311	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs35340841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35466062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35529204	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35574173	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4304839	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4353322	0.90[CHB][hapmap]
rs4502032	0.86[CHB][hapmap]
rs4561252	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4762969	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4762970	0.90[CHB][hapmap]
rs4762971	0.91[CHB][hapmap]
rs57544392	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs59143079	0.85[ASN][1000 genomes]
rs6487100	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6487101	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6487103	0.84[ASN][1000 genomes]
rs6487104	0.86[ASN][1000 genomes]
rs6487105	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs67369958	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7131827	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7303620	0.87[CHB][hapmap]
rs7308219	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308418	0.90[CHB][hapmap]
rs7316700	0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7487165	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7488735	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7488869	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7955323	0.87[ASN][1000 genomes]
rs7955819	0.84[ASN][1000 genomes]
rs7959560	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7969959	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 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	chr12:20660000-20665000	Strong transcription	Hela-S3	cervix
2	chr12:20660400-20664600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:20660800-20666600	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:20660800-20667600	Weak transcription	Fetal Heart	heart
5	chr12:20660800-20672800	Weak transcription	Fetal Intestine Large	intestine
6	chr12:20661200-20667600	Weak transcription	Aorta	Aorta
7	chr12:20661200-20673200	Weak transcription	NHDF-Ad	bronchial
8	chr12:20662000-20670600	Weak transcription	Osteobl	bone
9	chr12:20662200-20665600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:20662200-20670600	Weak transcription	Right Atrium	heart
11	chr12:20662400-20666000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:20662400-20674600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:20662600-20666400	Weak transcription	A549	lung
14	chr12:20663800-20664400	Enhancers	Left Ventricle	heart

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