Variant report

Variant	rs4946977
Chromosome Location	chr6:109775366-109775367
allele	C/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	EBF1	chr6:109775184-109775650	GM12878	blood:	n/a	chr6:109775526-109775535 chr6:109775524-109775535 chr6:109775524-109775537 chr6:109775525-109775535 chr6:109775526-109775535
2	CTCF	chr6:109775320-109775470	WI-38	lung:	n/a	n/a
3	EBF1	chr6:109775289-109775711	GM12878	blood:	n/a	chr6:109775526-109775535 chr6:109775524-109775535 chr6:109775524-109775537 chr6:109775525-109775535 chr6:109775526-109775535
4	POLR2A	chr6:109774791-109778612	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:109775261-109777757	GM19099	blood:	n/a	n/a
6	MTA3	chr6:109774944-109778262	GM12878	blood:	n/a	n/a
7	NRF1	chr6:109775226-109775537	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:109775300-109777378	NB4	blood:	n/a	n/a
9	POLR2A	chr6:109775074-109777912	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:109774855-109777633	GM12892	blood:	n/a	n/a
11	MAX	chr6:109775363-109777255	NB4	blood:	n/a	chr6:109776320-109776330 chr6:109776227-109776237
12	POLR2A	chr6:109774498-109777592	GM19193	blood:	n/a	n/a
13	STAT5A	chr6:109775299-109776940	GM12878	blood:	n/a	chr6:109776179-109776191 chr6:109776249-109776261
14	POLR2A	chr6:109774247-109777532	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:109775064-109777376	Raji	blood:	n/a	n/a
16	CTCF	chr6:109775247-109775547	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:109774772-109776119	Hela-S3	cervix:	n/a	n/a
18	CHD2	chr6:109775347-109777569	GM12878	blood:	n/a	chr6:109776252-109776262
19	POLR2A	chr6:109774576-109777618	GM18505	blood:	n/a	n/a
20	POLR2A	chr6:109775187-109776209	GM12891	blood:	n/a	n/a
21	POLR2A	chr6:109774967-109777662	GM18951	blood:	n/a	n/a
22	POLR2A	chr6:109774418-109779026	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:109775265-109775440	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:109775024-109779284	GM12891	blood:	n/a	n/a
25	POLR2A	chr6:109774366-109777650	GM12892	blood:	n/a	n/a
26	EBF1	chr6:109775245-109776907	GM12878	blood:	n/a	chr6:109775526-109775535 chr6:109775524-109775535 chr6:109775524-109775537 chr6:109775525-109775535 chr6:109775526-109775535
27	POLR2A	chr6:109774894-109775453	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:109774885-109777969	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:109774016..109776250-chr6:109801827..109803875,2	K562	blood:
2	chr6:109742234..109744237-chr6:109774891..109776518,2	MCF-7	breast:
3	chr6:109703058..109705958-chr6:109774873..109777253,2	MCF-7	breast:
4	chr6:109414902..109417715-chr6:109774468..109776378,2	K562	blood:
5	chr6:109702694..109704324-chr6:109775011..109776713,2	K562	blood:

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000183137	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000080546	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10080925	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs13437492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1476386	0.87[CEU][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs17070554	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17070590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1998813	0.86[CEU][hapmap]
rs2146411	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2177092	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2275649	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3757229	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3757237	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41288560	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946968	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4946971	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946975	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6907769	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs749621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs752260	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480934	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9480954	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9480959	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs9487074	0.86[CEU][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9487083	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487087	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487099	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487106	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487109	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
3	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
4	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
5	chr6:109763800-109775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:109763800-109775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:109763800-109775600	Weak transcription	HepG2	liver
8	chr6:109764400-109775800	Weak transcription	Hela-S3	cervix
9	chr6:109766600-109775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:109767000-109775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:109767000-109776000	Weak transcription	A549	lung
12	chr6:109767200-109776000	Weak transcription	Osteobl	bone
13	chr6:109768400-109775800	Weak transcription	Liver	Liver
14	chr6:109768400-109775800	Weak transcription	Left Ventricle	heart
15	chr6:109768400-109776000	Weak transcription	Ovary	ovary
16	chr6:109768400-109776400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:109768400-109776400	Weak transcription	K562	blood
18	chr6:109770600-109775400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:109771600-109775400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:109772000-109775600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:109772800-109775400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:109773000-109775400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:109773200-109775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:109773400-109775600	Enhancers	Primary hematopoietic stem cells	blood
25	chr6:109773400-109775600	Weak transcription	Aorta	Aorta
26	chr6:109773600-109775400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:109773800-109775400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:109773800-109775600	Enhancers	Fetal Thymus	thymus
29	chr6:109774000-109775600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:109774400-109775400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:109774400-109775400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:109774400-109775400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:109774400-109775400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:109774400-109775400	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr6:109774400-109775400	Genic enhancers	Fetal Intestine Small	intestine
36	chr6:109774400-109775600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:109774600-109775400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:109774600-109775400	Genic enhancers	Primary monocytes fromperipheralblood	blood
39	chr6:109774600-109775400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:109774600-109775400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:109774600-109775400	Genic enhancers	Brain Inferior Temporal Lobe	brain
42	chr6:109774600-109775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:109774600-109775600	Enhancers	Esophagus	oesophagus
44	chr6:109774600-109775800	Enhancers	Stomach Mucosa	stomach
45	chr6:109774800-109775400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:109774800-109775400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:109774800-109775400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:109774800-109775400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr6:109774800-109775400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:109774800-109775400	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon

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