Variant report

Variant	rs12594964
Chromosome Location	chr15:52900208-52900209
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	POLR2A	chr15:52900152-52900338	ProgFib	skin:	n/a	n/a

Variant related genes	Relation type
FAM214A	TF binding region

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

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

rs_ID	r²[population]
rs1080731	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10851520	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070909	0.91[ASN][1000 genomes]
rs11855616	0.81[ASN][1000 genomes]
rs13329393	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17651941	0.82[EUR][1000 genomes]
rs2414160	0.81[ASN][1000 genomes]
rs2414167	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28368342	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899492	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4390542	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4636853	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4776063	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55895733	0.81[EUR][1000 genomes]
rs7167494	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73396766	0.83[EUR][1000 genomes]
rs8030141	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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:109 , 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	chr15:52861800-52901600	Weak transcription	A549	lung
4	chr15:52861800-52908400	Weak transcription	Gastric	stomach
5	chr15:52861800-52934800	Weak transcription	Right Ventricle	heart
6	chr15:52862000-52901600	Weak transcription	Brain Angular Gyrus	brain
7	chr15:52869400-52945400	Weak transcription	Small Intestine	intestine
8	chr15:52870200-52905000	Weak transcription	HMEC	breast
9	chr15:52871200-52901600	Weak transcription	Dnd41	blood
10	chr15:52871800-52902200	Weak transcription	Fetal Brain Male	brain
11	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:52872200-52933800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:52872600-52920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:52873400-52928000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:52873800-52909600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr15:52874200-52917000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:52874800-52901200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:52874800-52944200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:52875400-52916200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:52878200-52909600	Strong transcription	Liver	Liver
21	chr15:52881400-52901600	Weak transcription	Psoas Muscle	Psoas
22	chr15:52882200-52920000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:52882400-52906200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr15:52882400-52926000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr15:52884200-52901600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:52884600-52901600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:52885600-52902000	Weak transcription	NHLF	lung
28	chr15:52885600-52903800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:52885600-52945200	Weak transcription	Spleen	Spleen
30	chr15:52886000-52901600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:52890600-52901600	Weak transcription	Pancreas	Pancrea
32	chr15:52890600-52906000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:52891200-52902000	Weak transcription	Lung	lung
34	chr15:52891200-52903800	Weak transcription	Fetal Intestine Small	intestine
35	chr15:52891400-52901600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:52891400-52927600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:52891600-52900600	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:52891600-52908400	Weak transcription	Aorta	Aorta
39	chr15:52892600-52901200	Weak transcription	HUVEC	blood vessel
40	chr15:52893800-52901600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:52894200-52901400	Weak transcription	NH-A	brain
42	chr15:52894400-52901200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:52894600-52904400	Strong transcription	Primary T cells from cord blood	blood
44	chr15:52894600-52906000	Strong transcription	Fetal Intestine Large	intestine
45	chr15:52894800-52900400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:52895400-52901600	Weak transcription	HepG2	liver
47	chr15:52895400-52902200	Weak transcription	Fetal Heart	heart
48	chr15:52895600-52901400	Weak transcription	HSMMtube	muscle
49	chr15:52896400-52900600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:52896400-52901200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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