Variant report

Variant	rs2653775
Chromosome Location	chr12:38938462-38938463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10047535	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10747520	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783208	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783220	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875653	0.82[ASN][1000 genomes]
rs11168117	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168173	0.86[ASN][1000 genomes]
rs11168929	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169037	0.82[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11169056	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11169105	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11169268	0.81[AMR][1000 genomes]
rs11183523	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11531207	0.82[EUR][1000 genomes]
rs11559976	0.82[ASN][1000 genomes]
rs1486342	0.84[ASN][1000 genomes]
rs1486343	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1486355	0.84[ASN][1000 genomes]
rs1564978	1.00[YRI][hapmap]
rs1684405	0.91[MEX][hapmap]
rs1719847	0.82[CEU][hapmap];0.95[JPT][hapmap]
rs2069210	0.82[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs2134398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455609	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2455610	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2630776	0.84[ASN][1000 genomes]
rs2630778	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2630780	0.84[ASN][1000 genomes]
rs2630782	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653722	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653738	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2653752	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2653754	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653760	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653761	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653769	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2730897	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2730901	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2730907	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2730908	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2730909	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2730910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2730944	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2730946	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2730948	0.84[ASN][1000 genomes]
rs2730949	0.84[ASN][1000 genomes]
rs2730954	0.85[EUR][1000 genomes]
rs2730955	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2730957	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2730964	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3924548	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4131569	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4354729	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4631924	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60368384	0.84[ASN][1000 genomes]
rs68075931	0.84[ASN][1000 genomes]
rs7304213	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7313048	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73269131	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7961649	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7964753	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7979853	0.82[ASN][1000 genomes]
rs826839	0.81[AMR][1000 genomes]
rs826840	0.83[AMR][1000 genomes]
rs826841	0.81[AMR][1000 genomes]
rs826853	0.82[CEU][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs826854	0.83[AMR][1000 genomes]
rs826857	0.81[AMR][1000 genomes]
rs826869	0.82[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs826871	0.81[AMR][1000 genomes]
rs826872	0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs826887	0.82[CEU][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs826890	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs826894	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs866120	0.82[CEU][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv898992	chr12:38106133-38959053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1047388	chr12:38169669-38949760	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv826332	chr12:38442547-38958438	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1046439	chr12:38453609-38956518	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv541475	chr12:38453609-38956518	Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	nsv916679	chr12:38805678-38963660	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1048325	chr12:38820721-38959645	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1040304	chr12:38908242-38995786	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1046817	chr12:38909036-38995330	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv469358	chr12:38919524-38989405	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv558582	chr12:38919524-38989405	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38936400-38938600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr12:38936400-38939000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr12:38936400-38939000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:38936800-38939000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:38936800-38939000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:38937200-38938600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr12:38937200-38938600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:38937200-38939000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:38937400-38939000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:38937400-38941000	Weak transcription	Hela-S3	cervix
11	chr12:38937800-38939000	Enhancers	Colon Smooth Muscle	Colon
12	chr12:38938200-38938600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:38938200-38938600	Enhancers	Rectal Smooth Muscle	rectum
14	chr12:38938200-38938800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:38938400-38938600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr12:38938400-38938800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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