Variant report

Variant	rs7602447
Chromosome Location	chr2:189919517-189919518
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	chr2:189914285..189915819-chr2:189918289..189921040,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10178611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178886	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10181597	1.00[ASW][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10194682	0.94[ASW][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10195184	0.83[ASN][1000 genomes]
rs11686253	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11690723	0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12622083	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12693526	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693527	0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693528	0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12989558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008197	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13391332	0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401377	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28486035	0.83[AFR][1000 genomes]
rs4667259	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6414121	0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434310	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434311	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434316	1.00[ASW][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434317	1.00[ASW][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434318	1.00[ASW][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434321	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434323	0.81[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6738371	1.00[ASW][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.94[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]
rs7420511	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7421040	0.94[ASW][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7421525	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7423808	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7423973	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424137	0.88[ASN][1000 genomes]
rs7424790	0.92[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7426169	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7557945	0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562299	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7568732	0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591905	0.80[AFR][1000 genomes]
rs7606293	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189889800-189931000	Weak transcription	Esophagus	oesophagus
2	chr2:189893200-189932600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:189894600-189932800	Weak transcription	Right Ventricle	heart
4	chr2:189895200-189940800	Strong transcription	HSMM	muscle
5	chr2:189895600-189965200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:189896200-189962400	Weak transcription	Left Ventricle	heart
7	chr2:189896400-189922600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:189896800-189932800	Weak transcription	Pancreas	Pancrea
9	chr2:189897000-189949000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:189897200-189934400	Weak transcription	Gastric	stomach
11	chr2:189897400-189932400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:189897600-189934000	Weak transcription	Lung	lung
13	chr2:189898400-189938200	Weak transcription	HMEC	breast
14	chr2:189899000-189925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:189899000-189939200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:189900800-189964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:189901200-189947400	Weak transcription	Fetal Brain Male	brain
18	chr2:189902400-189921600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:189902600-189937000	Strong transcription	NH-A	brain
20	chr2:189904000-189938200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:189904400-189921200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:189904400-189926800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:189904400-189934400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:189904400-189951000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:189904600-189932400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:189906400-189925400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:189907800-189929200	Weak transcription	Liver	Liver
28	chr2:189908000-189927800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:189909000-189921200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:189909200-189936200	Weak transcription	Small Intestine	intestine
31	chr2:189909800-189934200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:189911400-189919600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:189911400-189926600	Strong transcription	HSMMtube	muscle
34	chr2:189911800-189923400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:189912000-189921600	Strong transcription	NHLF	lung
36	chr2:189912400-189961600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:189912800-189931200	Weak transcription	Colonic Mucosa	Colon
38	chr2:189914000-189932800	Weak transcription	Fetal Kidney	kidney
39	chr2:189914400-189937000	Strong transcription	Adipose Nuclei	Adipose
40	chr2:189914800-189946800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:189915000-189921000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:189915000-189921000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:189915000-189924600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr2:189915000-189950600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:189915200-189921000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:189915400-189938200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:189915400-189951000	Strong transcription	Osteobl	bone
48	chr2:189915800-189919800	Strong transcription	Fetal Stomach	stomach
49	chr2:189915800-189923600	Strong transcription	A549	lung
50	chr2:189916200-189929200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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