Variant report

Variant	rs12664729
Chromosome Location	chr6:131948719-131948720
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	MYBL2	chr6:131948507-131949844	HepG2	liver:	n/a	n/a
2	SIN3A	chr6:131948548-131949779	H1-hESC	embryonic stem cell:	n/a	chr6:131949721-131949730
3	RAD21	chr6:131948664-131949911	SK-N-SH	brain:	n/a	chr6:131949621-131949635 chr6:131949536-131949555
4	GABPA	chr6:131948638-131949783	A549	lung:	n/a	n/a
5	POLR2A	chr6:131948522-131949576	MCF10A-Er-Src	breast:	n/a	n/a
6	GABPA	chr6:131948659-131949817	MCF-7	breast:	n/a	n/a
7	ZNF384	chr6:131948566-131949639	GM12878	blood:	n/a	n/a
8	E2F4	chr6:131948257-131948721	MCF10A-Er-Src	breast:	n/a	n/a
9	GABPA	chr6:131948706-131949774	SK-N-SH	brain:	n/a	n/a
10	MXI1	chr6:131948578-131949833	IMR90	lung:	n/a	n/a
11	JUN	chr6:131948694-131948968	HepG2	liver:	n/a	n/a
12	REST	chr6:131948692-131949900	H1-neurons	neurons:	n/a	chr6:131949720-131949730
13	SREBP2	chr6:131947542-131950211	GM12878	blood:	n/a	n/a
14	GABPA	chr6:131948490-131950034	MCF-7	breast:	n/a	n/a
15	ZNF384	chr6:131948568-131949702	K562	blood:	n/a	n/a
16	ESRRA	chr6:131948433-131950460	GM12878	blood:	n/a	n/a
17	CHD1	chr6:131948482-131949840	IMR90	lung:	n/a	chr6:131948857-131948864
18	IRF1	chr6:131948514-131949765	K562	blood:	n/a	chr6:131948707-131948721 chr6:131948709-131948720
19	MAZ	chr6:131948710-131949794	IMR90	lung:	n/a	chr6:131949077-131949086
20	SREBP1	chr6:131948381-131949907	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:131948713-131949770	SK-N-MC	brain:	n/a	n/a
22	HCFC1	chr6:131948459-131949805	Hela-S3	cervix:	n/a	n/a
23	JUN	chr6:131948620-131950372	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:131915943..131917882-chr6:131947988..131950710,2	K562	blood:
2	chr6:131945868..131955351-chr6:131956247..131968981,28	K562	blood:
3	chr6:131947988..131951073-chr6:131970793..131974788,3	MCF-7	breast:
4	chr6:131383272..131386235-chr6:131948272..131950497,3	MCF-7	breast:

Variant related genes	Relation type
ENPP3	TF binding region
ENSG00000252560	Chromatin interaction
ENSG00000154269	Chromatin interaction
ENSG00000079819	Chromatin interaction
ENSG00000112282	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2295446	1.00[CHB][hapmap]
rs6923189	1.00[CHB][hapmap]
rs7747145	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv515476	chr6:131615425-132228577	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv886668	chr6:131814865-131954797	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131925200-131948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:131936600-131948800	Weak transcription	Pancreas	Pancrea
3	chr6:131942400-131949000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:131945600-131948800	Weak transcription	Small Intestine	intestine
5	chr6:131945800-131948800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:131945800-131948800	Weak transcription	Esophagus	oesophagus
7	chr6:131945800-131948800	Weak transcription	Gastric	stomach
8	chr6:131945800-131948800	Weak transcription	Spleen	Spleen
9	chr6:131946200-131948800	Weak transcription	Left Ventricle	heart
10	chr6:131946200-131948800	Weak transcription	Lung	lung
11	chr6:131946200-131948800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:131947800-131948800	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr6:131947800-131948800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:131947800-131948800	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr6:131947800-131949600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:131947800-131949600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr6:131948000-131948800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:131948000-131948800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:131948000-131948800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:131948000-131948800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr6:131948000-131949600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:131948000-131949600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:131948000-131949600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:131948000-131949600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:131948000-131949600	Active TSS	NHDF-Ad	bronchial
26	chr6:131948000-131949800	Active TSS	NHLF	lung
27	chr6:131948000-131950000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:131948000-131950000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:131948000-131950000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:131948200-131948800	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr6:131948200-131948800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:131948200-131948800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:131948200-131949000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:131948200-131949400	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:131948200-131949600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:131948200-131949600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:131948200-131949600	Active TSS	GM12878-XiMat	blood
38	chr6:131948200-131949600	Active TSS	HMEC	breast
39	chr6:131948200-131949600	Active TSS	K562	blood
40	chr6:131948200-131949600	Active TSS	NH-A	brain
41	chr6:131948200-131949800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr6:131948200-131949800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:131948200-131950000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:131948200-131950000	Active TSS	Fetal Lung	lung
45	chr6:131948400-131948800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr6:131948400-131948800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:131948400-131948800	Flanking Active TSS	Liver	Liver
48	chr6:131948400-131948800	Active TSS	Brain Germinal Matrix	brain
49	chr6:131948400-131948800	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr6:131948400-131948800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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