Variant report

Variant	rs10516530
Chromosome Location	chr4:107019724-107019725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:101487184..101487847-chr4:107019665..107020665,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10004034	0.98[ASN][1000 genomes]
rs10017707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10025668	0.83[ASN][1000 genomes]
rs10155346	0.92[ASN][1000 genomes]
rs10516531	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11097923	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1134648	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11936196	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11938792	0.98[ASN][1000 genomes]
rs12500199	0.83[AMR][1000 genomes]
rs12508029	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512475	0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17036491	0.83[AMR][1000 genomes]
rs17036492	0.83[AMR][1000 genomes]
rs17036581	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1988966	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2212969	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28418378	0.83[ASN][1000 genomes]
rs28600991	0.92[ASN][1000 genomes]
rs3109952	0.93[ASN][1000 genomes]
rs3109954	0.93[ASN][1000 genomes]
rs3109956	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3109959	0.95[ASN][1000 genomes]
rs3113246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3113251	0.93[ASN][1000 genomes]
rs3133167	0.93[ASN][1000 genomes]
rs3133173	0.96[ASN][1000 genomes]
rs34305991	0.99[ASN][1000 genomes]
rs34909190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34923623	1.00[ASN][1000 genomes]
rs4415033	0.96[ASN][1000 genomes]
rs4441824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4533833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4560491	0.94[CHB][hapmap];0.98[ASN][1000 genomes]
rs4582218	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57983950	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533233	0.81[AMR][1000 genomes]
rs6533241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6533244	1.00[CHB][hapmap];0.84[JPT][hapmap];0.98[ASN][1000 genomes]
rs6836796	0.87[ASN][1000 genomes]
rs6848855	0.98[ASN][1000 genomes]
rs6853347	0.92[ASN][1000 genomes]
rs72960673	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7442226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7669347	0.84[ASN][1000 genomes]
rs7677394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7680756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7694217	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9884121	0.90[ASN][1000 genomes]
rs9991203	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs9993259	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3419151	chr4:106987397-107020894	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv1799793	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1801716	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1849248	chr4:107000462-107062671	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1850577	chr4:107000462-107062671	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106997200-107031000	Weak transcription	Psoas Muscle	Psoas
2	chr4:107010200-107025400	Weak transcription	Small Intestine	intestine
3	chr4:107012400-107024400	Weak transcription	Fetal Heart	heart
4	chr4:107012400-107026800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:107012600-107025000	Weak transcription	Brain Substantia Nigra	brain
6	chr4:107012600-107025200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:107012600-107026200	Weak transcription	Stomach Mucosa	stomach
8	chr4:107012600-107026600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:107012600-107026600	Weak transcription	GM12878-XiMat	blood
10	chr4:107012600-107026600	Weak transcription	HSMM	muscle
11	chr4:107012600-107026800	Weak transcription	Fetal Kidney	kidney
12	chr4:107012600-107029800	Weak transcription	Fetal Brain Male	brain
13	chr4:107012600-107029800	Weak transcription	Dnd41	blood
14	chr4:107012600-107031200	Weak transcription	Brain Angular Gyrus	brain
15	chr4:107012600-107033200	Weak transcription	Osteobl	bone
16	chr4:107012600-107033800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:107012600-107034400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:107012600-107038400	Weak transcription	NHDF-Ad	bronchial
19	chr4:107012800-107022200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:107012800-107024600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr4:107012800-107024600	Weak transcription	Brain Anterior Caudate	brain
22	chr4:107012800-107024800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:107012800-107024800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:107012800-107024800	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:107012800-107024800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:107012800-107025400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:107012800-107025400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:107012800-107026200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:107012800-107030600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:107012800-107031400	Weak transcription	HSMMtube	muscle
31	chr4:107012800-107033400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:107013000-107024600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:107013000-107031000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:107014000-107024600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:107014000-107024800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:107014000-107029800	Weak transcription	Brain Germinal Matrix	brain
37	chr4:107014000-107031000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:107014000-107031000	Weak transcription	Fetal Thymus	thymus
39	chr4:107014000-107031200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:107014000-107034600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr4:107014200-107024800	Weak transcription	Esophagus	oesophagus
42	chr4:107014200-107024800	Weak transcription	Fetal Intestine Large	intestine
43	chr4:107014200-107024800	Weak transcription	Placenta	Placenta
44	chr4:107014200-107024800	Weak transcription	Thymus	Thymus
45	chr4:107014200-107024800	Weak transcription	Spleen	Spleen
46	chr4:107014200-107025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:107014200-107025000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:107014200-107025000	Weak transcription	Aorta	Aorta
49	chr4:107014200-107025000	Weak transcription	Lung	lung
50	chr4:107014200-107025200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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