Variant report

Variant	rs12903617
Chromosome Location	chr15:52875828-52875829
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	chr15:52874167..52876909-chr15:52882421..52884748,2	MCF-7	breast:
2	chr15:52860389..52862379-chr15:52875369..52878722,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11853917	0.81[ASN][1000 genomes]
rs11857150	0.81[ASN][1000 genomes]
rs12102003	0.97[ASN][1000 genomes]
rs12902679	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12915981	0.81[ASN][1000 genomes]
rs17614559	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288271	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414161	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414163	0.82[ASN][1000 genomes]
rs2414166	0.81[ASN][1000 genomes]
rs35372377	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35505902	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751614	0.81[ASN][1000 genomes]
rs4774634	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4776058	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776059	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023352	0.84[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	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

No data

Chromatin state (count:104 , 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	chr15:52861400-52878600	Weak transcription	Ovary	ovary
3	chr15:52861400-52883600	Weak transcription	Lung	lung
4	chr15:52861600-52880600	Weak transcription	Fetal Intestine Small	intestine
5	chr15:52861600-52883800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:52861600-52884000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:52861600-52885000	Weak transcription	Spleen	Spleen
8	chr15:52861600-52901600	Weak transcription	Esophagus	oesophagus
9	chr15:52861800-52876000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:52861800-52876400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:52861800-52878600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:52861800-52882600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:52861800-52882600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:52861800-52883800	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:52861800-52884400	Weak transcription	Thymus	Thymus
16	chr15:52861800-52890600	Weak transcription	Fetal Kidney	kidney
17	chr15:52861800-52896800	Weak transcription	Hela-S3	cervix
18	chr15:52861800-52901600	Weak transcription	A549	lung
19	chr15:52861800-52908400	Weak transcription	Gastric	stomach
20	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
21	chr15:52862000-52901600	Weak transcription	Brain Angular Gyrus	brain
22	chr15:52866400-52889800	Weak transcription	Pancreas	Pancrea
23	chr15:52867400-52882400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:52869200-52880400	Weak transcription	Brain Germinal Matrix	brain
25	chr15:52869200-52890200	Weak transcription	Aorta	Aorta
26	chr15:52869400-52895000	Weak transcription	Fetal Heart	heart
27	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
28	chr15:52869600-52878000	Weak transcription	NHDF-Ad	bronchial
29	chr15:52869800-52900000	Strong transcription	Primary B cells from cord blood	blood
30	chr15:52870200-52883600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:52870200-52905000	Weak transcription	HMEC	breast
32	chr15:52870600-52883800	Weak transcription	NHLF	lung
33	chr15:52871200-52876000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:52871200-52890400	Weak transcription	GM12878-XiMat	blood
35	chr15:52871200-52901600	Weak transcription	Dnd41	blood
36	chr15:52871600-52876000	Weak transcription	Osteobl	bone
37	chr15:52871800-52879400	Strong transcription	Primary T cells from cord blood	blood
38	chr15:52871800-52902200	Weak transcription	Fetal Brain Male	brain
39	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:52872000-52878200	Weak transcription	Psoas Muscle	Psoas
41	chr15:52872000-52900200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr15:52872200-52877200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:52872200-52877400	Strong transcription	Liver	Liver
44	chr15:52872200-52883600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr15:52872200-52883800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:52872400-52876200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr15:52872400-52881600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr15:52872400-52884200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:52872400-52897800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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