Variant report

Variant	rs16828270
Chromosome Location	chr2:148872237-148872238
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	chr2:148869849..148872323-chr2:148885274..148887437,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10199458	0.81[EUR][1000 genomes]
rs10207309	0.83[EUR][1000 genomes]
rs10497026	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10497029	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11902430	0.81[EUR][1000 genomes]
rs12463554	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12465610	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12467336	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12469509	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12469621	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12470955	0.83[EUR][1000 genomes]
rs12472459	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12473564	0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12476827	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12691773	0.81[EUR][1000 genomes]
rs12691774	0.83[EUR][1000 genomes]
rs12691775	0.83[EUR][1000 genomes]
rs12691776	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12691777	0.82[EUR][1000 genomes]
rs12691779	0.83[EUR][1000 genomes]
rs12994607	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13001158	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13003171	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13006721	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13012455	0.86[ASN][1000 genomes]
rs13013887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13015552	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13015570	0.92[AMR][1000 genomes]
rs13015655	0.83[EUR][1000 genomes]
rs13021605	0.81[CHB][hapmap]
rs13029038	1.00[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13029714	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13032303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033664	0.88[ASN][1000 genomes]
rs13036250	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1449959	0.83[EUR][1000 genomes]
rs16828354	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1823447	0.83[EUR][1000 genomes]
rs1901014	0.83[EUR][1000 genomes]
rs1901810	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1901811	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2084578	0.83[EUR][1000 genomes]
rs2122386	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2382201	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2382211	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35283425	0.82[EUR][1000 genomes]
rs3764955	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4001	0.83[EUR][1000 genomes]
rs4436897	0.83[EUR][1000 genomes]
rs4972320	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4972322	0.96[CEU][hapmap]
rs4972329	0.83[EUR][1000 genomes]
rs4972332	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4972334	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183898	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6430289	0.83[EUR][1000 genomes]
rs6430292	0.83[EUR][1000 genomes]
rs6430295	0.81[EUR][1000 genomes]
rs6711686	0.83[EUR][1000 genomes]
rs6714672	0.81[EUR][1000 genomes]
rs6730641	0.81[EUR][1000 genomes]
rs71350069	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs72855232	0.85[ASN][1000 genomes]
rs7568811	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7574180	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580733	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7583759	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7592576	0.81[EUR][1000 genomes]
rs7595067	0.83[EUR][1000 genomes]
rs7595286	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598361	1.00[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7604592	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv817366	chr2:148727068-148879681	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1000852	chr2:148730825-148934986	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv535972	chr2:148730825-148934986	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv916766	chr2:148743880-148955720	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv875276	chr2:148844369-148996824	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv997674	chr2:148862630-148995570	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1007998	chr2:148866051-148995570	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 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	chr2:148854800-148874000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:148855800-148901000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:148861200-148889000	Weak transcription	Aorta	Aorta
4	chr2:148863000-148881600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:148864000-148881200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:148864600-148883200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:148864800-148880200	Weak transcription	Osteobl	bone
8	chr2:148865000-148880200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:148866200-148876400	Weak transcription	Fetal Lung	lung
10	chr2:148866600-148881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:148868200-148872800	Weak transcription	Primary T cells from cord blood	blood
12	chr2:148868400-148875400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:148868400-148876600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:148868600-148880000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:148869400-148888400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:148870000-148876200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:148871000-148888200	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links