Variant report

Variant	rs7961649
Chromosome Location	chr12:38901443-38901444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10047535	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747520	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783208	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783220	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875653	0.92[ASN][1000 genomes]
rs10880998	0.80[ASN][1000 genomes]
rs10881015	0.82[ASN][1000 genomes]
rs10881044	0.82[ASN][1000 genomes]
rs11168117	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168173	0.95[ASN][1000 genomes]
rs11169037	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs11169056	0.83[JPT][hapmap]
rs11183523	0.85[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap]
rs11183555	0.81[ASN][1000 genomes]
rs11183567	0.80[ASN][1000 genomes]
rs11183599	0.81[ASN][1000 genomes]
rs11183611	0.80[ASN][1000 genomes]
rs11183623	0.82[ASN][1000 genomes]
rs11183624	0.82[ASN][1000 genomes]
rs11183640	0.82[ASN][1000 genomes]
rs11183651	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11183653	0.82[ASN][1000 genomes]
rs11183667	0.82[ASN][1000 genomes]
rs11183669	0.82[ASN][1000 genomes]
rs11531207	0.82[ASN][1000 genomes]
rs11832065	0.81[ASN][1000 genomes]
rs12230331	0.82[ASN][1000 genomes]
rs12230677	0.82[ASN][1000 genomes]
rs12313147	0.80[ASN][1000 genomes]
rs12424219	0.82[ASN][1000 genomes]
rs12426104	0.82[ASN][1000 genomes]
rs2134398	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2455610	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2630778	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2653722	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653738	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2653752	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2653769	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2653775	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730897	0.85[ASN][1000 genomes]
rs2730901	0.83[ASN][1000 genomes]
rs2730907	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2730908	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2730909	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2730910	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2730944	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2730955	0.82[AMR][1000 genomes]
rs2730957	0.82[AMR][1000 genomes]
rs2730964	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3924548	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4131569	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4354729	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4631924	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72480102	0.81[ASN][1000 genomes]
rs7304213	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7313048	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7485262	0.82[ASN][1000 genomes]
rs7485926	0.82[ASN][1000 genomes]
rs7486256	0.82[ASN][1000 genomes]
rs7486693	0.81[ASN][1000 genomes]
rs7488727	0.81[ASN][1000 genomes]
rs7964753	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7979853	0.92[ASN][1000 genomes]
rs826887	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs826890	0.88[JPT][hapmap]
rs826894	1.00[CEU][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898986	chr12:38015951-38922227	ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1047550	chr12:38207030-38908242	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035850	chr12:38207030-38912512	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38896800-38901600	Weak transcription	Hela-S3	cervix
2	chr12:38899400-38901800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:38899800-38901600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:38900600-38902200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:38900800-38901800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:38901400-38902400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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