Variant report

Variant	rs3774933
Chromosome Location	chr4:103426339-103426340
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	MAFK	chr4:103424300-103426499	GM12878	blood:	n/a	chr4:103425229-103425244 chr4:103425878-103425889 chr4:103425740-103425751 chr4:103425738-103425752 chr4:103425878-103425889 chr4:103425735-103425750
2	FOS	chr4:103426224-103426365	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr4:103426035-103426497	Hela-S3	cervix:	n/a	chr4:103426202-103426213 chr4:103426336-103426347
4	FOS	chr4:103426241-103426343	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr4:103426104-103426468	HepG2	liver:	n/a	n/a
6	CEBPB	chr4:103426079-103426400	IMR90	lung:	n/a	chr4:103426202-103426213 chr4:103426336-103426347
7	ARID3A	chr4:103426031-103426436	HepG2	liver:	n/a	chr4:103426037-103426053 chr4:103426038-103426054
8	CHD1	chr4:103421479-103426461	GM12878	blood:	n/a	chr4:103422282-103422292 chr4:103423516-103423526 chr4:103422315-103422325
9	CEBPB	chr4:103426114-103426357	K562	blood:	n/a	chr4:103426202-103426213 chr4:103426336-103426347
10	CEBPB	chr4:103426047-103426416	HepG2	liver:	n/a	chr4:103426202-103426213 chr4:103426336-103426347
11	CEBPB	chr4:103426197-103426403	A549	lung:	n/a	chr4:103426202-103426213 chr4:103426336-103426347
12	FOXA2	chr4:103426147-103426384	HepG2	liver:	n/a	n/a
13	MAX	chr4:103426251-103426358	A549	lung:	n/a	n/a
14	STAT3	chr4:103426266-103426400	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103425524..103427364-chr4:103430743..103433529,2	MCF-7	breast:
2	chr4:103424918..103426820-chr4:103440847..103443260,2	K562	blood:
3	chr4:103426144..103427805-chr4:103429263..103431794,2	MCF-7	breast:
4	chr4:103424918..103427629-chr4:103441760..103444240,2	K562	blood:

Variant related genes	Relation type
ENSG00000260651	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1005819	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1020759	0.92[CEU][hapmap]
rs1020760	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11722146	0.91[JPT][hapmap]
rs11723120	0.90[JPT][hapmap]
rs118882	1.00[JPT][hapmap]
rs12509517	0.91[JPT][hapmap]
rs1585213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1585215	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1598859	0.90[JPT][hapmap]
rs1599961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17032705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs170731	1.00[JPT][hapmap]
rs1801	0.91[JPT][hapmap]
rs2168805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs230491	1.00[JPT][hapmap]
rs230492	1.00[JPT][hapmap]
rs230493	1.00[JPT][hapmap]
rs230495	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230496	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230498	1.00[JPT][hapmap]
rs230500	1.00[JPT][hapmap]
rs230504	1.00[JPT][hapmap]
rs230505	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230509	1.00[JPT][hapmap]
rs230514	1.00[JPT][hapmap]
rs230515	1.00[JPT][hapmap]
rs230516	1.00[JPT][hapmap]
rs230519	1.00[JPT][hapmap]
rs230520	1.00[JPT][hapmap]
rs230521	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230525	1.00[JPT][hapmap]
rs230526	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230528	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230529	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs230531	1.00[JPT][hapmap]
rs230532	1.00[JPT][hapmap]
rs230533	1.00[JPT][hapmap]
rs230534	1.00[JPT][hapmap]
rs230535	1.00[JPT][hapmap]
rs230539	0.95[JPT][hapmap]
rs230540	0.91[JPT][hapmap]
rs230541	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs230542	0.90[JPT][hapmap]
rs3755867	0.91[JPT][hapmap]
rs3774936	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3774938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774956	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3774959	0.90[JPT][hapmap]
rs3774963	0.90[JPT][hapmap]
rs3774964	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4235404	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4648011	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4648055	0.90[JPT][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.90[JPT][hapmap]
rs4698858	0.90[CEU][hapmap];0.89[JPT][hapmap]
rs4699030	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs747559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9790601	0.91[JPT][hapmap]
rs980455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103421600-103426400	Active TSS	Right Atrium	heart
2	chr4:103422000-103426400	Active TSS	HSMMtube	muscle
3	chr4:103422000-103430400	Active TSS	GM12878-XiMat	blood
4	chr4:103423000-103426800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chr4:103423800-103427600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:103423800-103430800	Weak transcription	Left Ventricle	heart
7	chr4:103423800-103431000	Weak transcription	Gastric	stomach
8	chr4:103423800-103439800	Weak transcription	Ovary	ovary
9	chr4:103423800-103439800	Weak transcription	Pancreas	Pancrea
10	chr4:103423800-103439800	Weak transcription	Spleen	Spleen
11	chr4:103423800-103445800	Weak transcription	Lung	lung
12	chr4:103424000-103446000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:103424200-103426400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr4:103424200-103427800	Enhancers	Brain Cingulate Gyrus	brain
15	chr4:103424600-103426400	Enhancers	Small Intestine	intestine
16	chr4:103424600-103428000	Enhancers	Brain Substantia Nigra	brain
17	chr4:103424600-103428800	Enhancers	Colon Smooth Muscle	Colon
18	chr4:103424800-103427000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:103424800-103433400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:103424800-103442400	Weak transcription	HSMM	muscle
21	chr4:103425000-103426400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr4:103425200-103426400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:103425200-103426400	Flanking Active TSS	Hela-S3	cervix
24	chr4:103425200-103427000	Enhancers	Liver	Liver
25	chr4:103425200-103427200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr4:103425200-103439800	Weak transcription	Right Ventricle	heart
27	chr4:103425200-103456400	Weak transcription	Osteobl	bone
28	chr4:103425400-103426400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:103425400-103426400	Enhancers	Brain Anterior Caudate	brain
30	chr4:103425400-103426400	Flanking Active TSS	HMEC	breast
31	chr4:103425400-103431200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:103425600-103426400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr4:103425600-103426400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:103425600-103426400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:103425600-103437200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr4:103425600-103448400	Weak transcription	Fetal Thymus	thymus
37	chr4:103425800-103426400	Enhancers	Psoas Muscle	Psoas
38	chr4:103425800-103426400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:103425800-103426400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr4:103425800-103428000	Enhancers	Primary B cells from cord blood	blood
41	chr4:103425800-103428000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:103425800-103433000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:103426000-103426400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:103426000-103426400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:103426000-103426400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:103426000-103426400	Enhancers	Adipose Nuclei	Adipose
47	chr4:103426000-103426400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr4:103426000-103426400	Enhancers	Duodenum Mucosa	Duodenum
49	chr4:103426000-103426400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr4:103426000-103427000	Weak transcription	Fetal Lung	lung

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