Variant report

Variant	rs12039867
Chromosome Location	chr1:79960871-79960872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10874038	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811462	0.83[ASN][1000 genomes]
rs12021904	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12025658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12026767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12026857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12027492	1.00[AMR][1000 genomes]
rs12027718	0.83[ASN][1000 genomes]
rs12027888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12027892	0.91[ASN][1000 genomes]
rs12028685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12029642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12030299	1.00[AMR][1000 genomes]
rs12034665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036690	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12036905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037641	1.00[AMR][1000 genomes]
rs12039488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12039920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12039923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12040121	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12040237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12041180	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12041732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12041849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12042159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044896	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046726	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047490	0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047951	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048746	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049068	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1603126	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17098662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17103209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17103314	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17103450	1.00[AMR][1000 genomes]
rs2088103	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000134	0.83[ASN][1000 genomes]
rs3000143	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000144	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000145	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000146	1.00[ASN][1000 genomes]
rs3000157	0.83[ASN][1000 genomes]
rs3015018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015069	0.83[ASN][1000 genomes]
rs7525048	1.00[AMR][1000 genomes]
rs9425165	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1012004	chr1:79945395-80096748	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv535017	chr1:79945395-80096748	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1012296	chr1:79945395-80300216	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1005022	chr1:79950774-80106902	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79959600-79962200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr1:79959800-79961400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:79960000-79963200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:79960600-79961400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:79960600-79961400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:79960600-79961600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:79960600-79961800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:79960600-79962800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:79960600-79964400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:79960800-79961200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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