Variant report

Variant	rs850965
Chromosome Location	chr12:42539218-42539219
allele	A/C/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	BACH1	chr12:42538606-42539221	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr12:42538038-42539285	Hela-S3	cervix:	n/a	chr12:42538561-42538571 chr12:42538746-42538755 chr12:42538558-42538568 chr12:42538555-42538565
3	POLR2A	chr12:42538244-42539252	U87	brain:	n/a	n/a
4	POLR2A	chr12:42538047-42539301	GM19099	blood:	n/a	n/a
5	POLR2A	chr12:42538251-42539718	PBDE	blood:	n/a	n/a
6	TBL1XR1	chr12:42538373-42539556	K562	blood:	n/a	n/a
7	POLR2A	chr12:42537957-42539336	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr12:42538541-42539296	HepG2	liver:	n/a	n/a
9	GTF2F1	chr12:42538526-42539390	K562	blood:	n/a	n/a
10	MAX	chr12:42538250-42539452	GM12878	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
11	POLR2A	chr12:42537266-42539525	Hela-S3	cervix:	n/a	n/a
12	BCL3	chr12:42538495-42539699	A549	lung:	n/a	chr12:42538554-42538567 chr12:42538556-42538569 chr12:42538553-42538566 chr12:42538503-42538512 chr12:42538559-42538572 chr12:42538562-42538571 chr12:42538563-42538576 chr12:42538523-42538536 chr12:42538559-42538568
13	ARID3A	chr12:42538586-42539219	K562	blood:	n/a	n/a
14	EP300	chr12:42538124-42539297	ECC-1	luminal epithelium:	n/a	chr12:42538519-42538535 chr12:42538719-42538735 chr12:42538558-42538567 chr12:42538561-42538570
15	POLR2A	chr12:42538439-42539671	K562	blood:	n/a	n/a
16	TBP	chr12:42538579-42539323	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:42537845-42539754	Raji	blood:	n/a	n/a
18	TBP	chr12:42538275-42539244	H1-hESC	embryonic stem cell:	n/a	n/a
19	BHLHE40	chr12:42538416-42539375	GM12878	blood:	n/a	chr12:42538556-42538572 chr12:42538554-42538570 chr12:42538553-42538569
20	TFAP2C	chr12:42537838-42539271	Hela-S3	cervix:	n/a	chr12:42538818-42538833
21	PML	chr12:42538276-42539218	GM12878	blood:	n/a	n/a
22	CBX3	chr12:42538497-42539742	K562	blood:	n/a	n/a
23	MTA3	chr12:42538490-42539603	GM12878	blood:	n/a	n/a
24	MAX	chr12:42537795-42539367	K562	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
25	RCOR1	chr12:42538467-42539795	K562	blood:	n/a	n/a
26	POLR2A	chr12:42538303-42539347	K562	blood:	n/a	n/a
27	TEAD4	chr12:42538400-42539740	K562	blood:	n/a	n/a
28	CREB1	chr12:42538269-42539255	HepG2	liver:	n/a	n/a
29	E2F6	chr12:42538511-42539393	H1-hESC	embryonic stem cell:	n/a	chr12:42538561-42538571 chr12:42538746-42538755 chr12:42538558-42538568 chr12:42538555-42538565
30	MAX	chr12:42538134-42539251	HCT-116	colon:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
31	MAX	chr12:42538448-42539270	A549	lung:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
32	POLR2A	chr12:42538046-42539317	MCF10A-Er-Src	breast:	n/a	n/a
33	MXI1	chr12:42536964-42539693	SK-N-SH	brain:	n/a	n/a
34	CEBPB	chr12:42538552-42539246	K562	blood:	n/a	n/a
35	JUND	chr12:42538117-42539779	K562	blood:	n/a	n/a
36	PML	chr12:42538344-42539260	K562	blood:	n/a	n/a
37	POLR2A	chr12:42538078-42539725	NB4	blood:	n/a	n/a
38	HEY1	chr12:42538192-42539275	K562	blood:	n/a	n/a
39	TCF12	chr12:42538262-42539894	A549	lung:	n/a	chr12:42539655-42539663
40	WRNIP1	chr12:42538635-42540104	GM12878	blood:	n/a	n/a
41	TCF7L2	chr12:42538345-42539376	Hela-S3	cervix:	n/a	chr12:42539268-42539282
42	POLR2A	chr12:42538267-42539262	K562	blood:	n/a	n/a
43	POLR2A	chr12:42538184-42539470	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr12:42538116-42539232	GM12892	blood:	n/a	n/a
45	MAX	chr12:42538158-42539441	MCF-7	breast:	n/a	chr12:42539128-42539138 chr12:42538509-42538519
46	KAP1	chr12:42538386-42539924	HEK293	kidney:	n/a	n/a
47	TEAD4	chr12:42538280-42539475	ECC-1	luminal epithelium:	n/a	n/a
48	EP300	chr12:42538532-42539299	GM12878	blood:	n/a	chr12:42538719-42538735 chr12:42538558-42538567 chr12:42538561-42538570
49	RUNX3	chr12:42538173-42539234	GM12878	blood:	n/a	n/a
50	MAX	chr12:42537651-42539394	K562	blood:	n/a	chr12:42539128-42539138 chr12:42538509-42538519

No.	Distal block	Cell Line	Cell type
1	chr12:42538608..42539586-chr6:26056616..26057177,2	NB4	blood:
2	chr12:42536858..42540358-chr12:42630016..42633914,10	MCF-7	breast:
3	chr12:42537136..42539433-chr12:42719521..42721782,2	K562	blood:
4	chr12:42537005..42540223-chr12:42630265..42633071,6	MCF-7	breast:
5	chr12:42537125..42540322-chr12:42717377..42722308,7	MCF-7	breast:
6	chr12:42537957..42540928-chr12:42622624..42625244,2	MCF-7	breast:
7	chr12:42537704..42540061-chr12:42725418..42727107,2	K562	blood:
8	chr12:42535865..42541158-chr12:42630084..42634162,10	K562	blood:
9	chr12:42536195..42540644-chr12:42629191..42634148,6	K562	blood:
10	chr12:42536402..42539877-chr12:42717128..42721445,5	MCF-7	breast:
11	chr12:42538708..42539351-chr17:73286140..73286679,2	NB4	blood:
12	chr12:42537508..42540547-chr12:42555328..42558210,3	MCF-7	breast:
13	chr12:42538702..42539493-chr17:54990934..54991901,2	NB4	blood:

Variant related genes	Relation type
GXYLT1	TF binding region
ENSG00000139168	Chromatin interaction
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000121060	Chromatin interaction
ENSG00000269367	Chromatin interaction
ENSG00000187837	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1009721	1.00[EUR][1000 genomes]
rs11118	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs11829542	1.00[EUR][1000 genomes]
rs11830248	1.00[EUR][1000 genomes]
rs11833381	1.00[EUR][1000 genomes]
rs1233989	1.00[EUR][1000 genomes]
rs1233991	1.00[EUR][1000 genomes]
rs1233993	1.00[EUR][1000 genomes]
rs1234007	1.00[EUR][1000 genomes]
rs1234031	1.00[EUR][1000 genomes]
rs1234041	1.00[EUR][1000 genomes]
rs1234103	1.00[EUR][1000 genomes]
rs1238283	1.00[EUR][1000 genomes]
rs1626596	1.00[EUR][1000 genomes]
rs1628339	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1683199	0.87[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1683203	1.00[EUR][1000 genomes]
rs1688846	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1688876	1.00[EUR][1000 genomes]
rs17091023	1.00[EUR][1000 genomes]
rs1873684	1.00[EUR][1000 genomes]
rs2639131	1.00[EUR][1000 genomes]
rs57435495	1.00[EUR][1000 genomes]
rs58229270	1.00[EUR][1000 genomes]
rs58676357	1.00[EUR][1000 genomes]
rs60314019	1.00[EUR][1000 genomes]
rs7305651	1.00[EUR][1000 genomes]
rs73270269	1.00[EUR][1000 genomes]
rs73278244	1.00[EUR][1000 genomes]
rs73278291	1.00[EUR][1000 genomes]
rs73280009	1.00[EUR][1000 genomes]
rs73280011	1.00[EUR][1000 genomes]
rs73281814	1.00[EUR][1000 genomes]
rs73281820	1.00[EUR][1000 genomes]
rs73281838	1.00[EUR][1000 genomes]
rs73281851	1.00[EUR][1000 genomes]
rs73281860	1.00[EUR][1000 genomes]
rs73281880	1.00[EUR][1000 genomes]
rs73281886	1.00[EUR][1000 genomes]
rs73281894	1.00[EUR][1000 genomes]
rs73283707	1.00[EUR][1000 genomes]
rs73283734	1.00[EUR][1000 genomes]
rs73283759	1.00[EUR][1000 genomes]
rs73283792	1.00[EUR][1000 genomes]
rs73283799	1.00[EUR][1000 genomes]
rs73285617	1.00[EUR][1000 genomes]
rs73285619	1.00[EUR][1000 genomes]
rs73285621	1.00[EUR][1000 genomes]
rs73285641	1.00[EUR][1000 genomes]
rs73285662	1.00[EUR][1000 genomes]
rs73285670	1.00[EUR][1000 genomes]
rs7970895	1.00[EUR][1000 genomes]
rs824690	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824696	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824698	1.00[EUR][1000 genomes]
rs824715	1.00[EUR][1000 genomes]
rs824719	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs824720	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs824721	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824723	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[EUR][1000 genomes]
rs824725	1.00[EUR][1000 genomes]
rs824727	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824729	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824731	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824732	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824733	1.00[EUR][1000 genomes]
rs824735	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824737	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs844045	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs850964	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv3327626	chr12:42537735-42540233	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42536800-42539400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:42537000-42539400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:42537000-42539600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:42537200-42539400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr12:42537200-42539400	Active TSS	Left Ventricle	heart
6	chr12:42537200-42539400	Active TSS	Right Atrium	heart
7	chr12:42537400-42539400	Active TSS	Fetal Muscle Trunk	muscle
8	chr12:42537400-42539600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:42537400-42539600	Active TSS	Colonic Mucosa	Colon
10	chr12:42537400-42540000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:42537600-42539400	Active TSS	Brain Germinal Matrix	brain
12	chr12:42537600-42539400	Active TSS	Fetal Brain Female	brain
13	chr12:42537600-42539400	Active TSS	Right Ventricle	heart
14	chr12:42537800-42539400	Active TSS	Gastric	stomach
15	chr12:42537800-42539600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:42537800-42539600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:42537800-42539600	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr12:42538000-42539400	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr12:42538000-42539600	Active TSS	Stomach Smooth Muscle	stomach
20	chr12:42538400-42539400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:42538400-42539400	Active TSS	Thymus	Thymus
22	chr12:42538600-42539400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:42538600-42539600	Flanking Bivalent TSS/Enh	Dnd41	blood
24	chr12:42538800-42539400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
25	chr12:42538800-42539400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr12:42538800-42539400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr12:42538800-42539400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:42538800-42539400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr12:42538800-42539400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:42538800-42539400	ZNF genes & repeats	Fetal Brain Male	brain
31	chr12:42538800-42539400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:42538800-42539400	Flanking Active TSS	Hela-S3	cervix
33	chr12:42538800-42539400	Flanking Active TSS	HUVEC	blood vessel
34	chr12:42538800-42539400	Flanking Active TSS	NH-A	brain
35	chr12:42538800-42539400	Flanking Active TSS	NHDF-Ad	bronchial
36	chr12:42538800-42539600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr12:42538800-42539600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr12:42538800-42539600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:42538800-42539600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:42538800-42539600	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr12:42538800-42539600	Flanking Active TSS	GM12878-XiMat	blood
42	chr12:42538800-42539800	Flanking Active TSS	K562	blood
43	chr12:42539000-42539400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:42539000-42539400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr12:42539000-42539400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:42539000-42539400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr12:42539000-42539400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr12:42539000-42539400	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr12:42539000-42539400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr12:42539000-42539400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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