Variant report

Variant	rs2653770
Chromosome Location	chr12:39006646-39006647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1021258	1.00[JPT][hapmap]
rs1038540	1.00[JPT][hapmap]
rs10747574	1.00[JPT][hapmap]
rs10875959	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875962	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10875963	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1095577	1.00[JPT][hapmap]
rs11168552	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168979	0.88[ASN][1000 genomes]
rs11169095	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11169407	1.00[JPT][hapmap]
rs12309958	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12318974	0.91[ASN][1000 genomes]
rs12322362	0.95[ASN][1000 genomes]
rs12580227	0.84[ASN][1000 genomes]
rs1472657	0.88[ASN][1000 genomes]
rs1486349	1.00[JPT][hapmap]
rs1486352	1.00[JPT][hapmap]
rs1486353	1.00[JPT][hapmap]
rs1502631	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1615569	1.00[JPT][hapmap]
rs1619885	1.00[JPT][hapmap]
rs1620594	1.00[JPT][hapmap]
rs1620655	0.95[JPT][hapmap]
rs1624751	1.00[JPT][hapmap]
rs1684420	0.89[JPT][hapmap]
rs1684421	1.00[JPT][hapmap]
rs1719846	0.95[JPT][hapmap]
rs1827459	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1843640	1.00[JPT][hapmap]
rs1847181	0.85[ASN][1000 genomes]
rs1906043	1.00[JPT][hapmap]
rs2101370	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2264357	0.90[ASN][1000 genomes]
rs2388058	1.00[JPT][hapmap]
rs2630779	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2653739	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2653757	0.89[ASN][1000 genomes]
rs2653762	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2653777	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2730891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2730911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2730923	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2730931	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2730938	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238079	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4293160	1.00[JPT][hapmap]
rs4767968	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5005131	1.00[JPT][hapmap]
rs7957523	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7976054	1.00[JPT][hapmap]
rs7980889	0.91[ASN][1000 genomes]
rs826878	0.90[JPT][hapmap]
rs826893	0.91[JPT][hapmap]
rs864324	0.91[JPT][hapmap]
rs923200	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9645814	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9805091	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1039179	chr12:38453609-39029275	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv541476	chr12:38453609-39029275	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv470285	chr12:38950082-39007749	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39005200-39007800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links