Variant report

Variant	rs11926251
Chromosome Location	chr3:17616737-17616738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SATB1-8	chr3:17616695-17616802	NONHSAT088552

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs11914537	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11914797	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11915560	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11916424	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916984	1.00[EUR][1000 genomes]
rs11921699	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11922861	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11923635	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11924147	1.00[EUR][1000 genomes]
rs11924560	1.00[EUR][1000 genomes]
rs11925226	1.00[EUR][1000 genomes]
rs11925353	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926087	1.00[EUR][1000 genomes]
rs11927232	1.00[EUR][1000 genomes]
rs11927283	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927967	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929046	1.00[EUR][1000 genomes]
rs11929521	1.00[EUR][1000 genomes]
rs12106899	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12106900	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12107061	1.00[EUR][1000 genomes]
rs12152509	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12185952	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2121261	1.00[ASN][1000 genomes]
rs28525383	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57352109	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58152540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58392667	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58777809	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58848058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58921548	1.00[EUR][1000 genomes]
rs59582994	0.87[AMR][1000 genomes]
rs59891221	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59960076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60245392	1.00[EUR][1000 genomes]
rs60459720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60662240	1.00[EUR][1000 genomes]
rs60803166	1.00[EUR][1000 genomes]
rs60838916	1.00[EUR][1000 genomes]
rs60940413	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61650046	1.00[EUR][1000 genomes]
rs61698855	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577595	1.00[EUR][1000 genomes]
rs6577629	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789382	1.00[EUR][1000 genomes]
rs6796915	1.00[EUR][1000 genomes]
rs73145898	1.00[EUR][1000 genomes]
rs73156379	1.00[EUR][1000 genomes]
rs73160940	0.87[AMR][1000 genomes]
rs73160942	0.87[AMR][1000 genomes]
rs73160943	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160950	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160951	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160957	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73160959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73160967	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73161427	1.00[EUR][1000 genomes]
rs73161452	1.00[EUR][1000 genomes]
rs73164768	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73164796	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165729	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165734	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165735	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73165740	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165752	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165764	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165771	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165774	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73165775	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165777	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73165779	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73165792	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73165798	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73166516	1.00[EUR][1000 genomes]
rs73166544	1.00[EUR][1000 genomes]
rs73167503	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73167510	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167513	1.00[EUR][1000 genomes]
rs73167514	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167523	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73167527	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73168748	1.00[EUR][1000 genomes]
rs73168752	1.00[EUR][1000 genomes]
rs73170844	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170845	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170855	1.00[EUR][1000 genomes]
rs73170858	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170877	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73170878	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73172909	1.00[EUR][1000 genomes]
rs73172914	1.00[EUR][1000 genomes]
rs73172924	1.00[EUR][1000 genomes]
rs7619879	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7620585	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621577	1.00[EUR][1000 genomes]
rs7630381	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7631803	1.00[EUR][1000 genomes]
rs7648122	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9680896	1.00[EUR][1000 genomes]
rs9754654	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9754657	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941993	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv915606	chr3:17357042-17668263	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv999460	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv536510	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17580000-17619400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:17596000-17619600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:17608000-17621600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:17608600-17621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:17610800-17619400	Weak transcription	A549	lung
6	chr3:17613400-17617200	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:17613600-17621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:17614800-17623400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:17615200-17619400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:17615600-17620200	Weak transcription	Primary B cells from cord blood	blood
11	chr3:17615800-17618200	Weak transcription	Esophagus	oesophagus
12	chr3:17615800-17619200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:17616000-17616800	Weak transcription	Ovary	ovary
14	chr3:17616000-17663600	Weak transcription	Left Ventricle	heart
15	chr3:17616400-17619600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links