Variant report

Variant	rs12475781
Chromosome Location	chr2:113916912-113916913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113912322..113918193-chr2:113953978..113958305,10	MCF-7	breast:
2	chr2:113916765..113917269-chr2:113934049..113934628,2	MCF-7	breast:
3	chr2:113916801..113918833-chr2:113943214..113944985,2	MCF-7	breast:
4	chr2:113916276..113917249-chr2:113934015..113934953,5	MCF-7	breast:
5	chr2:113914021..113918016-chr2:113931911..113937619,8	MCF-7	breast:
6	chr2:113916336..113917249-chr2:113934015..113934941,3	MCF-7	breast:
7	chr2:113900912..113903399-chr2:113916692..113918209,2	K562	blood:
8	chr2:113913769..113918338-chr2:113954843..113958220,11	MCF-7	breast:
9	chr2:113916877..113920304-chr2:113923250..113926364,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234174	Chromatin interaction
ENSG00000125637	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11123168	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12470101	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2121332	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130991	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2264096	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2264390	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099478	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs315942	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs315957	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315958	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6542118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542119	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542120	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721033	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6721720	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7608389	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608695	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs895495	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs902693	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs931471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113915400-113917200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
2	chr2:113915800-113917200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:113915800-113917200	Enhancers	Gastric	stomach
4	chr2:113915800-113917400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:113915800-113917400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr2:113916000-113917000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:113916000-113917000	Enhancers	Fetal Intestine Large	intestine
8	chr2:113916000-113917200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:113916000-113917200	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr2:113916000-113917200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:113916000-113917200	Enhancers	Esophagus	oesophagus
12	chr2:113916000-113917200	Enhancers	Stomach Mucosa	stomach
13	chr2:113916000-113917200	Enhancers	NHLF	lung
14	chr2:113916000-113917400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:113916000-113918800	Enhancers	Placenta	Placenta
16	chr2:113916000-113920000	Weak transcription	K562	blood
17	chr2:113916000-113920200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:113916000-113921600	Weak transcription	Colonic Mucosa	Colon
19	chr2:113916000-113922000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:113916000-113939000	Weak transcription	Right Atrium	heart
21	chr2:113916200-113917000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr2:113916200-113917200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:113916200-113917200	Flanking Active TSS	Liver	Liver
24	chr2:113916200-113917400	Weak transcription	Thymus	Thymus
25	chr2:113916200-113917400	Enhancers	HepG2	liver
26	chr2:113916200-113921800	Weak transcription	Small Intestine	intestine
27	chr2:113916200-113922800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:113916400-113917000	Enhancers	A549	lung
29	chr2:113916400-113917200	Enhancers	Primary T cells from cord blood	blood
30	chr2:113916400-113917200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:113916400-113920000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:113916600-113917200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:113916600-113917200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:113916600-113917200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr2:113916600-113917200	Enhancers	NH-A	brain
36	chr2:113916600-113917400	Enhancers	Duodenum Mucosa	Duodenum
37	chr2:113916600-113917400	Enhancers	HMEC	breast
38	chr2:113916600-113917600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:113916600-113917600	Enhancers	Pancreas	Pancrea
40	chr2:113916600-113921800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:113916600-113922400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:113916600-113924200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:113916800-113917000	Enhancers	Fetal Stomach	stomach
44	chr2:113916800-113917000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr2:113916800-113917200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:113916800-113917200	Enhancers	Lung	lung
47	chr2:113916800-113917400	Enhancers	NHEK	skin
48	chr2:113916800-113917600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:113916800-113920200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:113916800-113920200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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