Variant report

Variant	rs7975230
Chromosome Location	chr12:11707870-11707871
allele	G/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	POLR2A	chr12:11706778-11710160	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:11706837-11708074	GM12891	blood:	n/a	n/a
3	CTCF	chr12:11706643-11707978	A549	lung:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
4	POLR2A	chr12:11706813-11709512	GM12878	blood:	n/a	n/a
5	SMC3	chr12:11706791-11707937	SK-N-SH	brain:	n/a	chr12:11707060-11707074
6	POLR2A	chr12:11707502-11707974	GM12878	blood:	n/a	n/a
7	WRNIP1	chr12:11707765-11707879	GM12878	blood:	n/a	n/a
8	CHD1	chr12:11706945-11707941	GM12878	blood:	n/a	n/a
9	JUN	chr12:11707830-11708017	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:11707772-11708082	GM12891	blood:	n/a	n/a
11	MXI1	chr12:11706678-11707874	SK-N-SH	brain:	n/a	n/a
12	JUND	chr12:11707847-11707998	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:11707573-11708036	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000247157	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10491980	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054355	1.00[ASN][1000 genomes]
rs11054420	1.00[EUR][1000 genomes]
rs12296206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297330	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12304175	1.00[JPT][hapmap]
rs12306671	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12312814	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12318942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1641623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16934824	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16935059	1.00[ASN][1000 genomes]
rs16935084	1.00[ASN][1000 genomes]
rs1795551	1.00[JPT][hapmap]
rs55959071	1.00[EUR][1000 genomes]
rs56717408	1.00[ASN][1000 genomes]
rs58160049	1.00[EUR][1000 genomes]
rs59624591	1.00[EUR][1000 genomes]
rs59692713	1.00[EUR][1000 genomes]
rs60499077	1.00[EUR][1000 genomes]
rs61366849	1.00[EUR][1000 genomes]
rs7294334	1.00[EUR][1000 genomes]
rs7305726	1.00[EUR][1000 genomes]
rs7306490	1.00[EUR][1000 genomes]
rs7308344	1.00[EUR][1000 genomes]
rs7316082	1.00[ASN][1000 genomes]
rs73286612	1.00[ASN][1000 genomes]
rs73288732	1.00[EUR][1000 genomes]
rs73288733	1.00[EUR][1000 genomes]
rs73288736	1.00[EUR][1000 genomes]
rs73288738	1.00[EUR][1000 genomes]
rs73288740	1.00[EUR][1000 genomes]
rs73288746	1.00[EUR][1000 genomes]
rs73288748	1.00[EUR][1000 genomes]
rs73288753	1.00[EUR][1000 genomes]
rs73288756	1.00[EUR][1000 genomes]
rs73288757	1.00[EUR][1000 genomes]
rs73288764	1.00[EUR][1000 genomes]
rs74060969	1.00[EUR][1000 genomes]
rs74061000	1.00[EUR][1000 genomes]
rs74062355	1.00[EUR][1000 genomes]
rs74062357	1.00[EUR][1000 genomes]
rs74062364	1.00[EUR][1000 genomes]
rs7972959	1.00[ASN][1000 genomes]
rs7975331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11697400-11708600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:11699000-11709000	Weak transcription	Fetal Lung	lung
3	chr12:11706400-11708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:11706600-11708600	Enhancers	Primary T cells from cord blood	blood
5	chr12:11706800-11708200	Enhancers	Stomach Smooth Muscle	stomach
6	chr12:11706800-11708600	Enhancers	Colon Smooth Muscle	Colon
7	chr12:11706800-11708600	Enhancers	Rectal Smooth Muscle	rectum
8	chr12:11706800-11708800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:11706800-11708800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:11706800-11709400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:11706800-11709600	Enhancers	Dnd41	blood
12	chr12:11707200-11708000	Flanking Active TSS	GM12878-XiMat	blood
13	chr12:11707200-11708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:11707200-11708400	Weak transcription	Stomach Mucosa	stomach
15	chr12:11707200-11708600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:11707200-11708600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:11707200-11708600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:11707400-11708000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:11707400-11708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:11707400-11708400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:11707400-11708400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:11707400-11708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:11707400-11708400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:11707400-11708600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:11707400-11708600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:11707400-11708800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:11707400-11708800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:11707400-11709000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:11707600-11708000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr12:11707600-11708000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:11707600-11708000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:11707600-11708000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:11707600-11708000	Weak transcription	Fetal Thymus	thymus
34	chr12:11707600-11708200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:11707600-11708400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:11707600-11708400	Weak transcription	Aorta	Aorta
37	chr12:11707600-11709000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:11707800-11708200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:11707800-11708200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:11707800-11708200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:11707800-11708800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:11707800-11709000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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