Variant report

Variant	rs230541
Chromosome Location	chr4:103497785-103497786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103495819..103498669-chr4:103504146..103506135,2	MCF-7	breast:
2	chr4:103489104..103492778-chr4:103495068..103498574,4	MCF-7	breast:
3	chr4:103419957..103425638-chr4:103495824..103504548,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1020759	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1020760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11722146	1.00[JPT][hapmap]
rs11723120	1.00[JPT][hapmap]
rs118882	0.84[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs12509517	1.00[JPT][hapmap]
rs1585213	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1585215	0.91[JPT][hapmap]
rs1598859	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs1599961	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs17032705	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs170731	0.90[JPT][hapmap]
rs1801	1.00[JPT][hapmap]
rs2168805	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs230491	0.91[JPT][hapmap]
rs230492	0.90[JPT][hapmap]
rs230493	0.81[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs230495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs230496	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs230498	0.84[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs230500	0.84[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs230504	0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs230505	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230509	0.91[JPT][hapmap]
rs230514	0.91[JPT][hapmap]
rs230515	0.89[JPT][hapmap]
rs230516	0.89[JPT][hapmap]
rs230519	0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs230520	0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs230521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230525	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs230526	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230528	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230529	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230531	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs230532	0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs230533	0.91[JPT][hapmap]
rs230534	0.90[JPT][hapmap]
rs230535	0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs230539	0.86[JPT][hapmap]
rs230540	1.00[JPT][hapmap]
rs230542	0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs3755867	1.00[JPT][hapmap]
rs3774933	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3774936	0.91[JPT][hapmap]
rs3774937	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs3774938	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs3774956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3774959	0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs3774963	1.00[JPT][hapmap]
rs3774964	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs3817685	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs3821958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4235404	0.91[JPT][hapmap]
rs4648011	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs4648055	0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs4648058	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4648068	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs4698858	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4698861	0.81[JPT][hapmap]
rs4698863	0.81[JPT][hapmap]
rs4699030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs747559	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs9790601	1.00[JPT][hapmap]
rs980455	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103466800-103498600	Weak transcription	Placenta	Placenta
2	chr4:103469600-103498000	Weak transcription	Esophagus	oesophagus
3	chr4:103470000-103498000	Weak transcription	Fetal Stomach	stomach
4	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
5	chr4:103473600-103498000	Weak transcription	Aorta	Aorta
6	chr4:103476000-103498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:103476400-103498000	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:103476400-103498200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:103478200-103511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:103478600-103498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:103479200-103497800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:103482200-103498000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:103482200-103498800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:103482400-103498600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:103482800-103497800	Weak transcription	Fetal Intestine Large	intestine
16	chr4:103482800-103498000	Weak transcription	Fetal Intestine Small	intestine
17	chr4:103482800-103498200	Weak transcription	Brain Anterior Caudate	brain
18	chr4:103483000-103518600	Weak transcription	Small Intestine	intestine
19	chr4:103483200-103498000	Weak transcription	Right Ventricle	heart
20	chr4:103483200-103516600	Weak transcription	Brain Angular Gyrus	brain
21	chr4:103483400-103497800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:103483400-103498000	Weak transcription	Pancreas	Pancrea
23	chr4:103483400-103498200	Weak transcription	Left Ventricle	heart
24	chr4:103483400-103498200	Weak transcription	Ovary	ovary
25	chr4:103483400-103541600	Weak transcription	K562	blood
26	chr4:103484000-103498000	Weak transcription	Spleen	Spleen
27	chr4:103486000-103498000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:103486000-103498000	Weak transcription	Liver	Liver
29	chr4:103486000-103498000	Weak transcription	HSMMtube	muscle
30	chr4:103486400-103497800	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:103486600-103498200	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:103488200-103520000	Weak transcription	Fetal Kidney	kidney
33	chr4:103488400-103498000	Weak transcription	Colonic Mucosa	Colon
34	chr4:103488400-103498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:103488600-103498000	Weak transcription	Lung	lung
36	chr4:103488600-103498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:103488600-103498200	Weak transcription	Gastric	stomach
38	chr4:103488600-103498800	Weak transcription	Fetal Heart	heart
39	chr4:103488600-103498800	Weak transcription	Psoas Muscle	Psoas
40	chr4:103488800-103498000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:103488800-103498000	Weak transcription	NHDF-Ad	bronchial
42	chr4:103489000-103498000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:103489000-103498800	Weak transcription	HSMM	muscle
44	chr4:103489600-103498000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:103489800-103498000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:103490000-103498000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:103490600-103498000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:103490600-103498000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:103490800-103498200	Weak transcription	Fetal Lung	lung
50	chr4:103490800-103519200	Weak transcription	Stomach Mucosa	stomach

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