Variant report

Variant	rs9634171
Chromosome Location	chr12:117486221-117486222
allele	A/G
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	MYBL2	chr12:117485818-117486379	HepG2	liver:	n/a	n/a
2	ARID3A	chr12:117485974-117486354	HepG2	liver:	n/a	n/a
3	TCF12	chr12:117485964-117486351	HepG2	liver:	n/a	chr12:117486296-117486306 chr12:117486298-117486305
4	RXRA	chr12:117485882-117486390	HepG2	liver:	n/a	n/a
5	FOXA2	chr12:117485974-117486362	HepG2	liver:	n/a	n/a
6	HNF4A	chr12:117485955-117486310	HepG2	liver:	n/a	n/a
7	FOXA1	chr12:117485907-117486390	HepG2	liver:	n/a	n/a
8	FOXA2	chr12:117485922-117486460	A549	lung:	n/a	n/a
9	HEY1	chr12:117485807-117486383	HepG2	liver:	n/a	n/a
10	HDAC2	chr12:117485748-117486462	HepG2	liver:	n/a	n/a
11	FOXP2	chr12:117485800-117486312	PFSK-1	brain:	n/a	n/a
12	HNF4G	chr12:117485895-117486650	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:117485821-117486638	HepG2	liver:	n/a	n/a
14	MXI1	chr12:117485895-117486380	HepG2	liver:	n/a	n/a
15	NFIC	chr12:117485903-117486295	HepG2	liver:	n/a	n/a
16	EP300	chr12:117485844-117486357	HepG2	liver:	n/a	chr12:117486174-117486184
17	NR2F2	chr12:117485962-117486617	HepG2	liver:	n/a	n/a
18	RCOR1	chr12:117486092-117486440	HepG2	liver:	n/a	n/a
19	MBD4	chr12:117485846-117486698	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:117485589-117486905	HepG2	liver:	n/a	n/a
21	MAX	chr12:117485915-117486278	HepG2	liver:	n/a	n/a
22	HDAC2	chr12:117485795-117486440	HepG2	liver:	n/a	n/a
23	ELF1	chr12:117485889-117486315	HepG2	liver:	n/a	n/a
24	FOXA1	chr12:117485846-117486447	HepG2	liver:	n/a	n/a
25	FOXA1	chr12:117485799-117486381	HepG2	liver:	n/a	n/a
26	FOXP2	chr12:117485968-117486267	PFSK-1	brain:	n/a	n/a
27	YY1	chr12:117485775-117486254	HepG2	liver:	n/a	n/a
28	NFIC	chr12:117485837-117486311	HepG2	liver:	n/a	n/a
29	MAZ	chr12:117485992-117486291	HepG2	liver:	n/a	n/a
30	HNF4A	chr12:117485826-117486260	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:117485715-117486886	HL-60	blood:	n/a	n/a
32	EP300	chr12:117485779-117486397	HepG2	liver:	n/a	chr12:117486174-117486184
33	RFX5	chr12:117486067-117486248	HepG2	liver:	n/a	n/a
34	NR2F2	chr12:117485724-117486767	HepG2	liver:	n/a	n/a
35	FOXA2	chr12:117485745-117486944	HepG2	liver:	n/a	n/a
36	MYC	chr12:117486191-117486244	HepG2	liver:	n/a	n/a
37	FOXA1	chr12:117485831-117486402	HepG2	liver:	n/a	n/a
38	TEAD4	chr12:117485948-117486362	H1-hESC	embryonic stem cell:	n/a	chr12:117486142-117486151
39	RAD21	chr12:117485969-117486268	HepG2	liver:	n/a	n/a
40	SP1	chr12:117485857-117486383	HepG2	liver:	n/a	chr12:117486206-117486215
41	SRF	chr12:117486068-117486248	HepG2	liver:	n/a	n/a
42	TEAD4	chr12:117485825-117486431	HepG2	liver:	n/a	chr12:117486142-117486151
43	MYBL2	chr12:117485727-117486413	HepG2	liver:	n/a	n/a
44	FOXA2	chr12:117485982-117486427	A549	lung:	n/a	n/a

Variant related genes	Relation type
TESC	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10735100	0.94[JPT][hapmap]
rs10735101	0.94[JPT][hapmap]
rs10744887	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774895	0.94[JPT][hapmap]
rs10774898	0.82[CHD][hapmap];0.94[JPT][hapmap]
rs10774899	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850734	0.94[JPT][hapmap]
rs10850745	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850746	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850747	0.96[CEU][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850751	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850752	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068299	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068300	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068301	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068306	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611741	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11832441	0.84[EUR][1000 genomes]
rs11834817	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837022	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12368876	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472523	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2062528	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173654	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291911	0.88[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2291916	0.82[CHD][hapmap];0.94[JPT][hapmap]
rs2393124	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782191	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782192	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs4766816	0.94[JPT][hapmap]
rs4766823	0.94[JPT][hapmap]
rs4766825	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767477	0.94[JPT][hapmap]
rs55969361	0.84[EUR][1000 genomes]
rs58470318	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59756806	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490103	0.94[JPT][hapmap]
rs6490104	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490105	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6490106	0.92[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6490107	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7133090	0.94[JPT][hapmap]
rs7294692	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297303	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7486428	0.94[JPT][hapmap]
rs7953553	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956481	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960638	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960731	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964668	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964686	0.84[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7968761	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968891	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971795	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972416	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978810	0.82[CEU][hapmap];0.84[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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117479600-117488000	Enhancers	Fetal Heart	heart
2	chr12:117483600-117489200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:117483800-117487000	Genic enhancers	Spleen	Spleen
4	chr12:117483800-117488400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:117483800-117498000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:117483800-117498200	Weak transcription	Brain Angular Gyrus	brain
7	chr12:117483800-117498200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:117484000-117486400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:117484000-117487000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:117484000-117490000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:117484000-117490800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:117484000-117493600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:117484200-117486400	Weak transcription	Brain Anterior Caudate	brain
14	chr12:117484200-117486400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:117484200-117487400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:117484200-117488800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:117484400-117487400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr12:117484400-117489400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:117484400-117489600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:117484400-117490200	Weak transcription	Fetal Brain Female	brain
21	chr12:117484400-117497800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:117484600-117487200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr12:117484600-117487400	Strong transcription	Dnd41	blood
24	chr12:117484600-117487600	Weak transcription	Fetal Brain Male	brain
25	chr12:117484600-117488000	Weak transcription	Brain Germinal Matrix	brain
26	chr12:117484800-117486800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr12:117484800-117498200	Weak transcription	Thymus	Thymus
28	chr12:117485000-117487400	Genic enhancers	Pancreas	Pancrea
29	chr12:117485600-117486600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:117485600-117486800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:117485600-117487000	Bivalent Enhancer	Fetal Stomach	stomach
32	chr12:117485600-117487200	Enhancers	Placenta	Placenta
33	chr12:117485600-117487400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:117485600-117487400	Enhancers	Right Ventricle	heart
35	chr12:117485800-117486400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:117485800-117486400	Enhancers	Fetal Intestine Small	intestine
37	chr12:117485800-117486400	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr12:117485800-117486600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:117485800-117486600	Enhancers	Fetal Intestine Large	intestine
40	chr12:117485800-117486600	Enhancers	Fetal Lung	lung
41	chr12:117485800-117486600	Flanking Active TSS	HepG2	liver
42	chr12:117485800-117486600	Enhancers	NHLF	lung
43	chr12:117485800-117486600	Enhancers	Osteobl	bone
44	chr12:117485800-117486800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr12:117485800-117486800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:117485800-117486800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr12:117485800-117487000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr12:117485800-117487000	Enhancers	Lung	lung
49	chr12:117485800-117487200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:117485800-117487200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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