Variant report

Variant	rs10771925
Chromosome Location	chr12:9752730-9752731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10743780	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10743782	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771901	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771915	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771916	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771918	0.93[ASN][1000 genomes]
rs10771919	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771920	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844110	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10844135	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844140	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844141	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1135816	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11829861	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12579453	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2058426	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2058427	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2241005	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2241006	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2536929	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs28545519	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2888922	0.84[ASN][1000 genomes]
rs3933456	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763239	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763240	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763630	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763633	0.85[ASN][1000 genomes]
rs4763635	0.92[ASN][1000 genomes]
rs4763655	0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4764447	0.81[JPT][hapmap]
rs6488031	0.87[ASN][1000 genomes]
rs7137213	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7300782	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7301615	0.87[EUR][1000 genomes]
rs7955007	0.86[ASN][1000 genomes]
rs985911	0.95[ASN][1000 genomes]
rs985912	0.95[ASN][1000 genomes]
rs985913	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv898753	chr12:9644018-9755578	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv898754	chr12:9696687-9755578	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10771925	RP11-726G1.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10771925	RP11-726G1.1	cis	Artery Tibial	GTEx
rs10771925	RP11-726G1.1	cis	Artery Aorta	GTEx
rs10771925	RP11-22B23.1	cis	Artery Tibial	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9734400-9763000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:9736000-9760200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:9738200-9759600	Weak transcription	Primary T cells from cord blood	blood
4	chr12:9744600-9755800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:9745600-9755600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:9746000-9760000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:9746600-9756400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:9749200-9754200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:9750000-9759600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:9750400-9756800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr12:9751400-9758000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:9752000-9753400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:9752200-9753000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:9752200-9753200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:9752200-9753400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:9752400-9753000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr12:9752600-9753000	Enhancers	Fetal Intestine Large	intestine
18	chr12:9752600-9753000	Flanking Active TSS	A549	lung
19	chr12:9752600-9753200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:9752600-9753200	Enhancers	Fetal Intestine Small	intestine

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