Variant report

Variant	rs11949751
Chromosome Location	chr5:42569585-42569586
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	chr5:42557269..42559251-chr5:42568041..42570943,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10941578	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10941579	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739444	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11740415	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs11948453	1.00[JPT][hapmap]
rs11955075	1.00[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12516901	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12520276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12521020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160458	0.96[CEU][hapmap]
rs13176410	0.91[EUR][1000 genomes]
rs13184352	0.84[CEU][hapmap]
rs28943881	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374598	0.90[EUR][1000 genomes]
rs34466913	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34535288	0.93[EUR][1000 genomes]
rs34895721	0.86[EUR][1000 genomes]
rs35090794	0.90[EUR][1000 genomes]
rs4075783	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4242115	1.00[JPT][hapmap]
rs4305645	1.00[JPT][hapmap]
rs4314405	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4365846	0.96[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs4368736	0.92[EUR][1000 genomes]
rs4395642	0.96[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs4484445	1.00[JPT][hapmap]
rs4489074	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4493680	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4496716	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4504390	0.87[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4533898	0.92[ASN][1000 genomes]
rs4554233	1.00[JPT][hapmap]
rs4866791	1.00[JPT][hapmap]
rs4866936	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs55696942	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61197005	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6451626	1.00[JPT][hapmap]
rs6859653	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap]
rs6863381	0.85[CEU][hapmap]
rs6865492	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881929	1.00[CEU][hapmap];0.97[TSI][hapmap]
rs6887718	1.00[JPT][hapmap]
rs6896667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7703713	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs7707913	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7712701	0.95[EUR][1000 genomes]
rs7714392	0.95[EUR][1000 genomes]
rs7721816	1.00[JPT][hapmap]
rs7735889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736209	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42565800-42570200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:42565800-42571000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:42566000-42571000	Weak transcription	HMEC	breast
4	chr5:42566000-42571200	Weak transcription	Psoas Muscle	Psoas
5	chr5:42566000-42576200	Weak transcription	Spleen	Spleen
6	chr5:42566200-42571000	Weak transcription	NHEK	skin
7	chr5:42566200-42571200	Weak transcription	Left Ventricle	heart
8	chr5:42566800-42571000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:42567400-42571200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:42567600-42570800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:42567600-42571200	Weak transcription	Aorta	Aorta
12	chr5:42567800-42571000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:42568000-42571200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:42568000-42571400	Weak transcription	Adipose Nuclei	Adipose
15	chr5:42568000-42571400	Weak transcription	HSMMtube	muscle
16	chr5:42568000-42579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:42568000-42581400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:42568000-42582200	Weak transcription	Fetal Intestine Small	intestine
19	chr5:42568400-42570400	Weak transcription	Right Ventricle	heart
20	chr5:42568400-42571200	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:42568400-42571200	Weak transcription	Right Atrium	heart
22	chr5:42568400-42571200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:42568400-42571200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:42568400-42581800	Weak transcription	Fetal Stomach	stomach
25	chr5:42568400-42582800	Weak transcription	Ovary	ovary
26	chr5:42568600-42570000	Weak transcription	Fetal Heart	heart
27	chr5:42568800-42571200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:42568800-42571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:42569400-42571000	Weak transcription	Fetal Lung	lung
30	chr5:42569400-42572200	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links