Variant report

Variant	rs12373772
Chromosome Location	chr2:20430049-20430050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20311235..20314165-chr2:20429589..20432745,4	MCF-7	breast:
2	chr2:20429918..20432803-chr2:20436063..20439254,4	MCF-7	breast:
3	chr2:20430017..20433569-chr2:20434113..20437840,4	MCF-7	breast:
4	chr2:20338207..20341164-chr2:20430015..20431577,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10175853	0.96[CEU][hapmap]
rs10192042	0.96[CEU][hapmap]
rs1043400	0.84[CEU][hapmap]
rs10495704	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1106111	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11096648	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096649	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096650	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11888357	0.84[CEU][hapmap]
rs11895228	0.81[CEU][hapmap]
rs12373819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464428	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12472685	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13393733	0.81[AMR][1000 genomes]
rs13415389	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002090	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2007340	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2348703	0.81[CEU][hapmap]
rs34678899	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3732162	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732163	0.84[ASN][1000 genomes]
rs3732164	0.84[ASN][1000 genomes]
rs3755300	0.86[ASN][1000 genomes]
rs3771227	0.85[ASN][1000 genomes]
rs3771229	0.90[ASN][1000 genomes]
rs3771232	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3771233	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771236	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3771238	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3771239	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3771240	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771241	0.84[ASN][1000 genomes]
rs3771243	0.87[ASN][1000 genomes]
rs3771244	0.84[ASN][1000 genomes]
rs3771246	0.84[ASN][1000 genomes]
rs3771247	0.88[CEU][hapmap];0.93[CHB][hapmap]
rs3796066	0.81[CEU][hapmap]
rs3821219	0.85[ASN][1000 genomes]
rs57938873	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59129757	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109740	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62111433	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62123442	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6748274	0.84[CEU][hapmap]
rs72785203	0.90[ASN][1000 genomes]
rs72785204	0.90[ASN][1000 genomes]
rs72785206	0.90[ASN][1000 genomes]
rs72785217	0.81[AMR][1000 genomes]
rs72785218	0.81[AMR][1000 genomes]
rs7558833	0.96[CEU][hapmap]
rs7563245	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7585590	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9306890	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798036	chr2:20423264-20442631	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv1846193	chr2:20423264-20442631	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1849406	chr2:20423264-20442631	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1819683	chr2:20423264-20455467	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20425800-20431000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:20425800-20431000	Weak transcription	NH-A	brain
3	chr2:20426000-20430600	Weak transcription	Hela-S3	cervix
4	chr2:20426000-20447000	Weak transcription	GM12878-XiMat	blood
5	chr2:20426200-20431000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:20426200-20431000	Weak transcription	Colonic Mucosa	Colon
7	chr2:20426200-20431000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:20426200-20431000	Weak transcription	A549	lung
9	chr2:20426200-20431200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:20426200-20431200	Weak transcription	Gastric	stomach
11	chr2:20426200-20436600	Weak transcription	Pancreas	Pancrea
12	chr2:20426400-20430400	Weak transcription	NHEK	skin
13	chr2:20426400-20430600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:20426400-20430800	Weak transcription	Esophagus	oesophagus
15	chr2:20426400-20430800	Weak transcription	HepG2	liver
16	chr2:20426400-20431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:20426400-20431000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:20426400-20431000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:20426400-20431200	Weak transcription	Fetal Intestine Large	intestine
20	chr2:20426400-20436800	Enhancers	Placenta	Placenta
21	chr2:20426600-20431000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:20427400-20431800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:20427800-20430400	Weak transcription	HMEC	breast
24	chr2:20428000-20431200	Weak transcription	Osteobl	bone
25	chr2:20428200-20431000	Weak transcription	Spleen	Spleen
26	chr2:20428800-20430400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:20429200-20430400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:20429400-20430400	Enhancers	NHDF-Ad	bronchial
29	chr2:20430000-20431000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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