Variant report

Variant	rs12227966
Chromosome Location	chr12:25305673-25305674
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10505959	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs10771166	0.86[CHB][hapmap]
rs10771171	0.83[ASN][1000 genomes]
rs10771174	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10771175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842464	0.86[CHB][hapmap]
rs10842468	0.86[JPT][hapmap]
rs10842470	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10842472	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10842476	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10842483	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10842488	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10842491	0.92[ASN][1000 genomes]
rs10842495	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842515	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs10842516	0.89[CEU][hapmap];0.84[JPT][hapmap]
rs10842517	0.89[CEU][hapmap];0.84[JPT][hapmap]
rs11047843	0.84[EUR][1000 genomes]
rs11047852	0.83[ASN][1000 genomes]
rs11047858	0.84[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11047862	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11047885	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11047912	1.00[JPT][hapmap]
rs11047914	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs11047917	0.86[JPT][hapmap]
rs11834088	0.86[CHB][hapmap]
rs12228638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12367971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425900	0.84[JPT][hapmap]
rs17388587	1.00[JPT][hapmap]
rs17389103	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2220196	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2883030	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3924650	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4313666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368021	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs4589388	0.82[ASN][1000 genomes]
rs55950027	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487458	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7133640	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs7134616	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7135130	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7303373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303669	1.00[CHB][hapmap]
rs7309670	0.82[JPT][hapmap]
rs7315339	1.00[JPT][hapmap]
rs7956818	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7960428	0.88[CHB][hapmap]
rs7960917	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7971062	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7971288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7973365	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973450	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7973623	0.94[CEU][hapmap]
rs7975271	1.00[CHB][hapmap]
rs7976254	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7980769	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic 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	22 gene(s)	inside rSNPs	diseases
6	nsv557796	chr12:25266203-25306458	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv515612	chr12:25272027-25341177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv557797	chr12:25272027-25341177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25304000-25305800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:25304000-25307400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:25304400-25305800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:25304400-25305800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr12:25304400-25305800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:25304400-25305800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:25304600-25305800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:25304600-25305800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr12:25304600-25305800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr12:25304600-25315600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:25305000-25308000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:25305200-25307600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:25305200-25307800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:25305200-25307800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:25305200-25307800	Weak transcription	NHDF-Ad	bronchial
16	chr12:25305200-25308000	Weak transcription	A549	lung
17	chr12:25305200-25308200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:25305400-25307800	Weak transcription	NHEK	skin
19	chr12:25305400-25308000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:25305400-25308000	Weak transcription	Fetal Lung	lung
21	chr12:25305400-25308000	Weak transcription	Hela-S3	cervix
22	chr12:25305600-25305800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:25305600-25308000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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