Variant report

Variant	rs28961346
Chromosome Location	chr2:51933674-51933675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10201408	0.96[ASN][1000 genomes]
rs11125373	0.93[ASN][1000 genomes]
rs11562944	0.96[ASN][1000 genomes]
rs11562969	0.91[ASN][1000 genomes]
rs11563021	0.91[ASN][1000 genomes]
rs11563088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11563089	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11563117	0.86[ASN][1000 genomes]
rs11563267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11884304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11891933	0.96[ASN][1000 genomes]
rs11896915	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12104790	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12105215	0.86[ASN][1000 genomes]
rs12475198	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1516184	0.98[ASN][1000 genomes]
rs1516186	0.96[ASN][1000 genomes]
rs2354387	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2354388	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2354389	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs28949269	0.93[ASN][1000 genomes]
rs28960993	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28961313	0.87[ASN][1000 genomes]
rs28961316	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28961321	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28961322	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28961332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28961340	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28961578	0.91[ASN][1000 genomes]
rs28961580	0.91[ASN][1000 genomes]
rs28961587	0.91[ASN][1000 genomes]
rs28961626	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28962184	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28965475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs28967868	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28967880	0.96[ASN][1000 genomes]
rs4108601	0.91[ASN][1000 genomes]
rs72888302	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001552	chr2:51225970-52139741	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv535708	chr2:51225970-52139741	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv874069	chr2:51723107-52006583	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1011738	chr2:51731251-51976068	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv516396	chr2:51914354-51934748	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv874077	chr2:51914354-51934748	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1008696	chr2:51920617-51949532	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1832597	chr2:51922567-51934748	Flanking Active TSS Weak transcription Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv581900	chr2:51922567-51934748	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv874078	chr2:51922567-51934748	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv1832378	chr2:51926599-51934748	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv581908	chr2:51926599-51934748	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv1793616	chr2:51926599-51935326	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv581909	chr2:51926599-51935797	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:51932600-51934600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:51933600-51934000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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