Variant report

Variant	rs62023352
Chromosome Location	chr15:52889448-52889449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52542793..52545085-chr15:52889244..52891733,2	MCF-7	breast:
2	chr15:52888619..52891451-chr15:53020250..53023070,2	MCF-7	breast:
3	chr15:52888487..52890518-chr15:52930804..52932790,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10851521	0.83[ASN][1000 genomes]
rs11070907	0.85[ASN][1000 genomes]
rs11853917	0.90[ASN][1000 genomes]
rs11857150	0.90[ASN][1000 genomes]
rs11858743	0.87[ASN][1000 genomes]
rs12102003	0.81[ASN][1000 genomes]
rs12898644	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12903617	0.84[ASN][1000 genomes]
rs12914047	0.82[ASN][1000 genomes]
rs12914502	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12915981	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17614559	0.84[ASN][1000 genomes]
rs1863512	0.82[AMR][1000 genomes]
rs2288271	0.84[ASN][1000 genomes]
rs2414161	0.84[ASN][1000 genomes]
rs2414163	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2414166	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34431049	0.87[ASN][1000 genomes]
rs35372377	0.84[ASN][1000 genomes]
rs35505902	0.84[ASN][1000 genomes]
rs3751614	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4774636	0.84[ASN][1000 genomes]
rs4776058	0.84[ASN][1000 genomes]
rs4776059	0.84[ASN][1000 genomes]
rs4776065	0.87[ASN][1000 genomes]
rs4776066	0.87[ASN][1000 genomes]
rs4776068	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8026800	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs933860	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1977718	chr15:52889192-52889613	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv3439572	chr15:52889291-52889479	Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52861200-52925200	Weak transcription	Stomach Mucosa	stomach
2	chr15:52861600-52901600	Weak transcription	Esophagus	oesophagus
3	chr15:52861800-52890600	Weak transcription	Fetal Kidney	kidney
4	chr15:52861800-52896800	Weak transcription	Hela-S3	cervix
5	chr15:52861800-52901600	Weak transcription	A549	lung
6	chr15:52861800-52908400	Weak transcription	Gastric	stomach
7	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
8	chr15:52862000-52901600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:52866400-52889800	Weak transcription	Pancreas	Pancrea
10	chr15:52869200-52890200	Weak transcription	Aorta	Aorta
11	chr15:52869400-52895000	Weak transcription	Fetal Heart	heart
12	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
13	chr15:52869800-52900000	Strong transcription	Primary B cells from cord blood	blood
14	chr15:52870200-52905000	Weak transcription	HMEC	breast
15	chr15:52871200-52890400	Weak transcription	GM12878-XiMat	blood
16	chr15:52871200-52901600	Weak transcription	Dnd41	blood
17	chr15:52871800-52902200	Weak transcription	Fetal Brain Male	brain
18	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:52872000-52900200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:52872400-52897800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:52872600-52890200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:52872600-52891000	Weak transcription	HUVEC	blood vessel
24	chr15:52872600-52920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:52873400-52928000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:52873600-52898800	Strong transcription	Adipose Nuclei	Adipose
27	chr15:52873800-52909600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr15:52874200-52900000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:52874200-52917000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:52874800-52893200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr15:52874800-52901200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:52875400-52916200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:52875800-52894800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:52878200-52909600	Strong transcription	Liver	Liver
36	chr15:52878600-52898400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:52879400-52895800	Weak transcription	Colonic Mucosa	Colon
38	chr15:52880800-52898000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:52881400-52901600	Weak transcription	Psoas Muscle	Psoas
40	chr15:52882200-52920000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr15:52882400-52906200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:52882400-52926000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:52883000-52897200	Strong transcription	Placenta	Placenta
44	chr15:52883200-52891200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:52884200-52901600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:52884600-52890000	Weak transcription	Ovary	ovary
47	chr15:52884600-52893800	Weak transcription	NH-A	brain
48	chr15:52884600-52901600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:52885000-52891000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:52885200-52894800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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