Variant report

Variant	rs9878937
Chromosome Location	chr3:100597989-100597990
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100595522..100598378-chr3:100600055..100603377,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1017438	0.87[ASN][1000 genomes]
rs1017439	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs11720318	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs13079711	0.87[CHB][hapmap]
rs1370160	0.85[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs1370161	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1436941	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs1816567	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1821794	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1836986	0.85[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs1836987	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1836988	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs2118170	1.00[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2118171	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2118172	0.90[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs2317331	0.84[CEU][hapmap]
rs3821725	0.85[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4328836	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4928057	0.87[CHB][hapmap]
rs4928093	0.84[CEU][hapmap];0.86[GIH][hapmap];0.80[EUR][1000 genomes]
rs4928095	0.81[EUR][1000 genomes]
rs62277104	0.87[ASN][1000 genomes]
rs6441555	0.89[EUR][1000 genomes]
rs6778625	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786325	0.85[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6786332	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6793103	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68184622	0.87[ASN][1000 genomes]
rs9290245	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs975536	0.90[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]

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	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100583800-100603400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:100589200-100599000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:100593200-100601600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:100594400-100598000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:100594400-100599000	Weak transcription	Psoas Muscle	Psoas
6	chr3:100594400-100618200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:100594600-100598600	Weak transcription	HSMMtube	muscle
8	chr3:100594600-100598800	Weak transcription	NHLF	lung
9	chr3:100594600-100616800	Weak transcription	Ovary	ovary
10	chr3:100594800-100598000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:100594800-100598000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:100594800-100598400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:100594800-100598600	Weak transcription	NHDF-Ad	bronchial
14	chr3:100594800-100599800	Weak transcription	Hela-S3	cervix
15	chr3:100595000-100598600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:100595200-100600000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:100595400-100599200	Weak transcription	Osteobl	bone
18	chr3:100596800-100599200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:100597400-100598600	Enhancers	Colon Smooth Muscle	Colon
20	chr3:100597400-100599600	Enhancers	Fetal Muscle Leg	muscle
21	chr3:100597600-100600200	Enhancers	Adipose Nuclei	Adipose
22	chr3:100597800-100598200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:100597800-100599200	Enhancers	Stomach Smooth Muscle	stomach
24	chr3:100597800-100599800	Enhancers	Fetal Lung	lung
25	chr3:100597800-100599800	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links