Variant report

Variant	rs230539
Chromosome Location	chr4:103495532-103495533
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	FOXP2	chr4:103495403-103495839	SK-N-MC	brain:	n/a	n/a
2	REST	chr4:103495483-103495838	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr4:103495376-103496001	HL-60	blood:	n/a	n/a
4	CEBPB	chr4:103495445-103495731	IMR90	lung:	n/a	n/a
5	SIN3AK20	chr4:103495508-103495715	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr4:103495395-103495930	SK-N-MC	brain:	n/a	n/a
7	SPI1	chr4:103495410-103495922	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103495247..103497005-chr4:103498545..103500219,2	K562	blood:
2	chr4:103493829..103496471-chr4:103690009..103691867,2	K562	blood:
3	chr4:103489104..103492778-chr4:103495068..103498574,4	MCF-7	breast:

Variant related genes	Relation type
NFKB1	TF binding region
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1005819	0.87[JPT][hapmap]
rs1020760	0.87[JPT][hapmap]
rs11722146	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs118882	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12509517	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1585213	0.95[JPT][hapmap]
rs1585215	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1599961	0.95[JPT][hapmap]
rs1609798	0.82[CHB][hapmap]
rs17032683	1.00[YRI][hapmap]
rs17032705	0.95[JPT][hapmap]
rs170731	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1801	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.91[JPT][hapmap]
rs230491	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230492	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230495	0.95[JPT][hapmap]
rs230496	0.95[JPT][hapmap]
rs230498	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230500	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230504	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230505	0.95[JPT][hapmap]
rs230509	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230511	0.96[CEU][hapmap]
rs230514	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230515	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs230516	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230519	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230520	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230521	0.95[JPT][hapmap]
rs230525	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230526	0.95[JPT][hapmap]
rs230528	0.95[JPT][hapmap]
rs230529	0.95[JPT][hapmap]
rs230531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230532	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230533	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230534	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230535	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs230541	0.86[JPT][hapmap]
rs230542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2903281	1.00[YRI][hapmap]
rs3755867	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs3774933	0.95[JPT][hapmap]
rs3774936	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3774937	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3774938	0.95[JPT][hapmap]
rs3774956	0.90[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3774963	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3774964	0.86[JPT][hapmap]
rs3817685	0.90[JPT][hapmap]
rs3821958	0.87[JPT][hapmap]
rs4235404	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	0.95[JPT][hapmap]
rs4648055	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs4648058	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4648068	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs4698858	0.84[JPT][hapmap]
rs4698861	0.83[CEU][hapmap]
rs4699030	0.86[JPT][hapmap]
rs747559	0.95[JPT][hapmap]
rs9790601	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs980455	0.95[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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103443200-103496000	Weak transcription	A549	lung
2	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:103461600-103496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:103466800-103498600	Weak transcription	Placenta	Placenta
5	chr4:103467000-103495600	Weak transcription	HepG2	liver
6	chr4:103469600-103498000	Weak transcription	Esophagus	oesophagus
7	chr4:103470000-103498000	Weak transcription	Fetal Stomach	stomach
8	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
9	chr4:103473600-103498000	Weak transcription	Aorta	Aorta
10	chr4:103475000-103496600	Weak transcription	HUVEC	blood vessel
11	chr4:103475200-103496400	Weak transcription	Hela-S3	cervix
12	chr4:103476000-103498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:103476400-103498000	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:103476400-103498200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:103478200-103511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:103478600-103498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:103479200-103497800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:103482200-103498000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:103482200-103498800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:103482400-103498600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:103482800-103496600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:103482800-103497800	Weak transcription	Fetal Intestine Large	intestine
23	chr4:103482800-103498000	Weak transcription	Fetal Intestine Small	intestine
24	chr4:103482800-103498200	Weak transcription	Brain Anterior Caudate	brain
25	chr4:103483000-103518600	Weak transcription	Small Intestine	intestine
26	chr4:103483200-103498000	Weak transcription	Right Ventricle	heart
27	chr4:103483200-103516600	Weak transcription	Brain Angular Gyrus	brain
28	chr4:103483400-103497800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:103483400-103498000	Weak transcription	Pancreas	Pancrea
30	chr4:103483400-103498200	Weak transcription	Left Ventricle	heart
31	chr4:103483400-103498200	Weak transcription	Ovary	ovary
32	chr4:103483400-103541600	Weak transcription	K562	blood
33	chr4:103484000-103498000	Weak transcription	Spleen	Spleen
34	chr4:103486000-103498000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:103486000-103498000	Weak transcription	Liver	Liver
36	chr4:103486000-103498000	Weak transcription	HSMMtube	muscle
37	chr4:103486200-103496200	Weak transcription	NH-A	brain
38	chr4:103486400-103497800	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:103486600-103498200	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:103488200-103520000	Weak transcription	Fetal Kidney	kidney
41	chr4:103488400-103498000	Weak transcription	Colonic Mucosa	Colon
42	chr4:103488400-103498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:103488600-103498000	Weak transcription	Lung	lung
44	chr4:103488600-103498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:103488600-103498200	Weak transcription	Gastric	stomach
46	chr4:103488600-103498800	Weak transcription	Fetal Heart	heart
47	chr4:103488600-103498800	Weak transcription	Psoas Muscle	Psoas
48	chr4:103488800-103496400	Weak transcription	Brain Substantia Nigra	brain
49	chr4:103488800-103497600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:103488800-103498000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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