Variant report

Variant	rs10208525
Chromosome Location	chr2:189904203-189904204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189896472..189898491-chr2:189903751..189905640,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10194770	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs10194927	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10195023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10197596	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10200215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207407	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10207530	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10210319	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931391	0.92[CEU][hapmap]
rs10931393	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs11186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392501	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13393368	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs13421883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28384143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55965240	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974662	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56074008	0.89[EUR][1000 genomes]
rs56954312	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56970084	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59777852	0.89[EUR][1000 genomes]
rs72902328	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902330	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72904403	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72904488	0.89[EUR][1000 genomes]
rs72906383	0.88[EUR][1000 genomes]
rs72915321	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72915330	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72915335	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355694	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355697	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7421172	0.85[CEU][hapmap]
rs7425327	0.92[CEU][hapmap]
rs7425816	0.89[CEU][hapmap]

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	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189888000-189917400	Weak transcription	Ovary	ovary
2	chr2:189889800-189931000	Weak transcription	Esophagus	oesophagus
3	chr2:189891600-189913600	Weak transcription	Fetal Kidney	kidney
4	chr2:189893200-189932600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:189893600-189916200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:189894000-189913800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:189894600-189932800	Weak transcription	Right Ventricle	heart
8	chr2:189895200-189909000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:189895200-189940800	Strong transcription	HSMM	muscle
10	chr2:189895600-189965200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:189896000-189907400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:189896200-189962400	Weak transcription	Left Ventricle	heart
13	chr2:189896400-189922600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:189896600-189910600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:189896800-189932800	Weak transcription	Pancreas	Pancrea
16	chr2:189897000-189911000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:189897000-189949000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:189897200-189934400	Weak transcription	Gastric	stomach
19	chr2:189897400-189905800	Weak transcription	Brain Anterior Caudate	brain
20	chr2:189897400-189917400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:189897400-189932400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:189897600-189934000	Weak transcription	Lung	lung
23	chr2:189898400-189938200	Weak transcription	HMEC	breast
24	chr2:189899000-189905000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:189899000-189916000	Weak transcription	Aorta	Aorta
26	chr2:189899000-189919000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:189899000-189925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:189899000-189939200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:189900800-189964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:189901000-189914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:189901000-189919000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:189901200-189947400	Weak transcription	Fetal Brain Male	brain
33	chr2:189901400-189909000	Strong transcription	HSMMtube	muscle
34	chr2:189901600-189907200	Strong transcription	Adipose Nuclei	Adipose
35	chr2:189901600-189908000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr2:189901600-189911000	Strong transcription	A549	lung
37	chr2:189902000-189910600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr2:189902200-189904400	Weak transcription	Primary T cells from cord blood	blood
39	chr2:189902400-189921600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:189902600-189906400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:189902600-189911200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:189902600-189914600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:189902600-189937000	Strong transcription	NH-A	brain
44	chr2:189902800-189905000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:189902800-189905400	Strong transcription	Fetal Stomach	stomach
46	chr2:189902800-189907600	Strong transcription	Fetal Intestine Large	intestine
47	chr2:189902800-189908000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:189902800-189908000	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr2:189902800-189908200	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:189902800-189914400	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links