Variant report

Variant	rs9880749
Chromosome Location	chr3:178731197-178731198
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:178726976..178728535-chr3:178731027..178733316,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11711320	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720081	0.91[EUR][1000 genomes]
rs1542	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2699887	0.80[CEU][hapmap]
rs2699905	0.80[CEU][hapmap]
rs4245914	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4279147	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280676	0.91[EUR][1000 genomes]
rs4315724	0.91[EUR][1000 genomes]
rs4337680	0.91[EUR][1000 genomes]
rs4377525	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4395442	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4417911	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4425305	0.88[ASN][1000 genomes]
rs4469018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501160	0.91[EUR][1000 genomes]
rs4505756	0.91[EUR][1000 genomes]
rs4522816	0.89[EUR][1000 genomes]
rs4525914	0.88[EUR][1000 genomes]
rs4552405	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4579062	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607155	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626139	0.91[EUR][1000 genomes]
rs4632588	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637331	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955796	0.91[EUR][1000 genomes]
rs4955802	0.89[EUR][1000 genomes]
rs4955807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115013	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56154408	0.89[EUR][1000 genomes]
rs6443607	0.88[EUR][1000 genomes]
rs6443614	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443617	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6443618	0.88[AMR][1000 genomes]
rs6772028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784495	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs6789706	0.87[EUR][1000 genomes]
rs6790867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793769	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793893	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794165	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6794956	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795238	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800015	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7429173	0.91[EUR][1000 genomes]
rs7612363	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7639391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643052	0.89[EUR][1000 genomes]
rs7651510	0.91[EUR][1000 genomes]
rs7652668	0.90[EUR][1000 genomes]
rs7652946	0.91[EUR][1000 genomes]
rs9830482	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831543	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9835752	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9835765	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846511	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9860318	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860749	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878734	0.97[ASN][1000 genomes]
rs9879637	0.91[EUR][1000 genomes]
rs9968179	0.85[CEU][hapmap]

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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178708800-178737800	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:178716400-178755000	Weak transcription	Pancreas	Pancrea
3	chr3:178717400-178744400	Weak transcription	HMEC	breast
4	chr3:178719200-178737600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:178719600-178733000	Weak transcription	Primary T cells from cord blood	blood
6	chr3:178720400-178734200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:178720600-178737600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:178721400-178737800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:178721400-178738000	Weak transcription	Aorta	Aorta
10	chr3:178722200-178751600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:178723000-178732000	Weak transcription	HSMM	muscle
12	chr3:178723000-178733600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:178723200-178731200	Weak transcription	HSMMtube	muscle
14	chr3:178723400-178749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:178723800-178754200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:178727800-178738000	Weak transcription	Fetal Heart	heart
17	chr3:178730600-178731400	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links