Variant report

Variant	rs6580664
Chromosome Location	chr12:38936062-38936063
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10506126	0.82[JPT][hapmap]
rs10783317	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs10783319	0.89[ASN][1000 genomes]
rs10783333	0.82[JPT][hapmap]
rs10875684	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10875817	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875944	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875945	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875950	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875951	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875953	0.81[JPT][hapmap]
rs10875961	0.91[ASN][1000 genomes]
rs10876008	0.83[JPT][hapmap]
rs11168202	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11168802	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168978	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169054	0.83[JPT][hapmap]
rs11169086	0.91[ASN][1000 genomes]
rs11169087	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11169094	0.91[ASN][1000 genomes]
rs11169258	0.82[JPT][hapmap]
rs11514109	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12314639	0.83[JPT][hapmap]
rs12368548	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12424190	0.82[JPT][hapmap]
rs1386018	0.83[JPT][hapmap]
rs1472658	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1486341	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1564978	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1875610	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2062758	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2220267	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2387982	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2387983	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759139	0.82[JPT][hapmap]
rs4073360	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4508240	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4616077	0.82[JPT][hapmap]
rs4768225	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768240	0.90[ASN][1000 genomes]
rs6580640	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6580697	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580718	0.80[CEU][hapmap];0.91[ASN][1000 genomes]
rs7294397	0.91[ASN][1000 genomes]
rs7960616	0.83[JPT][hapmap]
rs7970273	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7971075	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7976704	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9739497	0.90[ASN][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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38936000-38936600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:38936000-38938000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr12:38936000-38938400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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