Variant report

Variant	rs7980636
Chromosome Location	chr12:40029726-40029727
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10047563	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10219652	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10444570	0.89[JPT][hapmap]
rs10735885	0.88[JPT][hapmap]
rs10747825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747878	0.85[JPT][hapmap]
rs10783969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs10783993	0.91[EUR][1000 genomes]
rs10783998	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10784001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10784016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs10784019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10784051	0.88[JPT][hapmap]
rs10784059	0.89[JPT][hapmap]
rs10877335	0.92[EUR][1000 genomes]
rs10877337	0.91[EUR][1000 genomes]
rs10877369	0.88[EUR][1000 genomes]
rs10877383	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10877410	0.87[EUR][1000 genomes]
rs11172998	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11173257	0.87[EUR][1000 genomes]
rs11173260	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs11173262	0.90[EUR][1000 genomes]
rs11173376	0.87[EUR][1000 genomes]
rs11173394	0.86[EUR][1000 genomes]
rs11173401	0.86[EUR][1000 genomes]
rs11173423	0.86[EUR][1000 genomes]
rs11173424	0.86[EUR][1000 genomes]
rs11173428	0.86[EUR][1000 genomes]
rs11173433	0.86[EUR][1000 genomes]
rs11173434	0.86[EUR][1000 genomes]
rs11173440	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs11173446	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs11173459	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs11173494	0.91[CEU][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs11173507	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs11173541	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs11173550	0.89[JPT][hapmap]
rs11173551	0.83[EUR][1000 genomes]
rs11173553	0.82[EUR][1000 genomes]
rs11532458	0.80[EUR][1000 genomes]
rs12229203	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs12229301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12229418	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs12230687	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs12823801	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12825223	0.90[EUR][1000 genomes]
rs4077987	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4129365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap]
rs4238072	0.89[JPT][hapmap]
rs4238073	0.89[JPT][hapmap]
rs4312128	0.89[JPT][hapmap]
rs4337105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4357762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4405390	0.89[JPT][hapmap]
rs4411336	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4417381	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4417382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs4495951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4594067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs4767949	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4768166	0.92[CEU][hapmap]
rs4768168	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4768169	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4768170	0.89[EUR][1000 genomes]
rs57244766	0.87[EUR][1000 genomes]
rs58418587	0.89[EUR][1000 genomes]
rs58755301	0.84[EUR][1000 genomes]
rs61931185	0.86[EUR][1000 genomes]
rs61931208	0.86[EUR][1000 genomes]
rs61933102	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61933154	0.89[EUR][1000 genomes]
rs61933157	0.86[EUR][1000 genomes]
rs61933158	0.86[EUR][1000 genomes]
rs6421191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6421195	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6421196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs6421197	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6421198	0.92[EUR][1000 genomes]
rs6581250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6581263	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6581265	0.92[EUR][1000 genomes]
rs6581266	0.92[EUR][1000 genomes]
rs6581270	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs6581271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs6581272	0.92[EUR][1000 genomes]
rs6581294	0.89[EUR][1000 genomes]
rs7136929	0.88[EUR][1000 genomes]
rs7296585	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7301886	0.86[EUR][1000 genomes]
rs7485345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7486196	0.83[EUR][1000 genomes]
rs7486621	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7486631	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs7487999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7956577	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7959905	0.92[EUR][1000 genomes]
rs7961070	0.92[EUR][1000 genomes]
rs7961346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325166	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv899020	chr12:39985206-40040331	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv899021	chr12:39989172-40053423	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv899022	chr12:40014427-40111761	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 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	chr12:40022000-40036800	Weak transcription	K562	blood
2	chr12:40029600-40032400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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