Variant report

Variant	rs162262
Chromosome Location	chr3:78905076-78905077
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	chr3:78896368..78899171-chr3:78904358..78907500,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1355983	0.81[YRI][hapmap]
rs162263	0.83[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs162264	0.86[CHB][hapmap]
rs162265	0.92[CHB][hapmap]
rs162268	0.86[CHB][hapmap]
rs162423	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[YRI][hapmap]
rs162425	0.95[CEU][hapmap];0.92[CHB][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs162426	0.85[EUR][1000 genomes]
rs162427	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162428	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162429	0.96[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs186688	0.86[CHB][hapmap]
rs328045	0.83[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs328047	0.86[CHB][hapmap];0.85[MEX][hapmap]
rs329805	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs329811	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs329812	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs329813	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs329814	0.86[CHB][hapmap];0.82[TSI][hapmap]
rs329816	0.86[CHB][hapmap]
rs329818	0.81[ASN][1000 genomes]
rs329819	0.88[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs329822	0.86[CHB][hapmap]
rs329824	0.85[EUR][1000 genomes]
rs329825	0.92[CHB][hapmap]
rs331134	0.82[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs331139	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331143	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331145	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs331149	0.86[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs331158	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes]
rs331161	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331162	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331163	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs331164	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs331181	0.82[ASN][1000 genomes]
rs331182	0.87[EUR][1000 genomes]
rs331188	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331189	0.84[ASN][1000 genomes]
rs331190	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs331199	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs369346	0.86[CHB][hapmap]
rs379346	0.86[CHB][hapmap]
rs387900	0.86[CHB][hapmap]
rs432141	0.86[EUR][1000 genomes]
rs4681013	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs479956	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs498805	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs531125	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6548601	0.86[CHB][hapmap]
rs6772919	0.86[CHB][hapmap]
rs6800782	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs7610996	0.88[YRI][hapmap]
rs7617538	0.86[CHB][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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78896600-78908400	Weak transcription	Osteobl	bone
2	chr3:78897200-78907200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:78898600-78906800	Weak transcription	A549	lung
4	chr3:78899200-78906800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:78900800-78906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:78904200-78905800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:78904400-78905400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:78904400-78906800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:78904600-78905600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:78904600-78906600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:78904600-78906600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:78904600-78908000	Weak transcription	Fetal Kidney	kidney
13	chr3:78904800-78905200	Flanking Active TSS	HUVEC	blood vessel
14	chr3:78904800-78905400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:78904800-78905400	Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:78904800-78905600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:78904800-78906800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:78904800-78907000	Weak transcription	HSMM	muscle
19	chr3:78905000-78905200	Weak transcription	Fetal Lung	lung
20	chr3:78905000-78905400	Weak transcription	HepG2	liver
21	chr3:78905000-78905600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:78905000-78906200	Weak transcription	NHEK	skin

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