Variant report

Variant	rs2653738
Chromosome Location	chr12:39019372-39019373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10047535	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10160990	0.82[CEU][hapmap]
rs10747520	0.81[ASN][1000 genomes]
rs10783208	0.81[ASN][1000 genomes]
rs10783220	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1095573	0.85[CEU][hapmap]
rs1095576	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168117	0.85[EUR][1000 genomes]
rs11168173	0.81[ASN][1000 genomes]
rs11168929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169037	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169056	0.83[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169105	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169268	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169324	0.81[AMR][1000 genomes]
rs11559976	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12231800	0.86[EUR][1000 genomes]
rs1486342	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1486343	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1486355	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1523119	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1523120	0.83[EUR][1000 genomes]
rs1533918	0.85[CEU][hapmap]
rs1615648	0.85[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1621487	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1684397	0.84[EUR][1000 genomes]
rs1719833	0.85[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs1719847	0.85[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2069210	0.85[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2134398	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2455609	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2455610	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2630776	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2630778	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2630780	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2630782	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653722	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653752	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653754	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653760	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653761	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653769	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653775	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2730897	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2730901	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2730907	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730908	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730909	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2730944	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2730946	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730948	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730949	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730954	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2730955	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730957	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2730964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924548	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4131569	0.81[ASN][1000 genomes]
rs4354729	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4631924	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60368384	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61221058	0.82[AFR][1000 genomes]
rs68075931	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304213	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7313048	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73269131	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961649	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7964753	0.85[EUR][1000 genomes]
rs8181763	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8181765	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826839	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs826840	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs826841	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs826845	0.84[AMR][1000 genomes]
rs826847	0.84[AMR][1000 genomes]
rs826849	0.85[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs826853	0.82[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs826854	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs826857	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs826860	0.95[JPT][hapmap]
rs826861	0.85[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs826862	0.85[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs826867	0.82[EUR][1000 genomes]
rs826868	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs826869	0.85[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs826871	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs826872	0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs826880	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826884	0.82[CEU][hapmap]
rs826887	0.82[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826890	0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs826894	1.00[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs826895	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826896	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs851933	0.95[JPT][hapmap]
rs862331	0.82[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs862332	0.84[AMR][1000 genomes]
rs866120	0.82[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39018600-39020000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:39019000-39019600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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