Variant report

Variant	rs12067490
Chromosome Location	chr1:57987455-57987456
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10493226	1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10493227	1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10493229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889057	1.00[EUR][1000 genomes]
rs11207047	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs11207048	0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11207049	1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11207050	1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11207051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11207053	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207054	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11803909	0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11804717	1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11805586	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810273	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12063594	0.96[YRI][hapmap];0.98[AFR][1000 genomes]
rs12065019	1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12067444	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072932	1.00[AMR][1000 genomes]
rs12073810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12073879	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs1341311	1.00[EUR][1000 genomes]
rs1524706	1.00[EUR][1000 genomes]
rs1524712	1.00[EUR][1000 genomes]
rs1524731	1.00[EUR][1000 genomes]
rs1534048	1.00[EUR][1000 genomes]
rs1815685	1.00[EUR][1000 genomes]
rs1880442	1.00[EUR][1000 genomes]
rs1935045	1.00[EUR][1000 genomes]
rs2204376	1.00[EUR][1000 genomes]
rs2265623	1.00[EUR][1000 genomes]
rs2691430	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2691431	0.90[AFR][1000 genomes]
rs2691433	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2691434	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2691443	1.00[EUR][1000 genomes]
rs2691444	1.00[EUR][1000 genomes]
rs2691445	1.00[EUR][1000 genomes]
rs2691447	1.00[EUR][1000 genomes]
rs2691448	1.00[EUR][1000 genomes]
rs2691452	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2691453	0.90[AFR][1000 genomes]
rs2691455	1.00[EUR][1000 genomes]
rs2691467	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs2793621	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2793622	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs2793623	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2793641	1.00[EUR][1000 genomes]
rs2793642	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2793644	0.81[YRI][hapmap]
rs2793645	0.90[AFR][1000 genomes]
rs2805850	1.00[EUR][1000 genomes]
rs2805851	1.00[EUR][1000 genomes]
rs2805881	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2805882	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs28391765	1.00[EUR][1000 genomes]
rs28621926	1.00[EUR][1000 genomes]
rs4310463	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4348747	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4526638	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529731	1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553222	1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4554738	1.00[EUR][1000 genomes]
rs56721199	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56873272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58873103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59078890	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60116819	1.00[EUR][1000 genomes]
rs60867983	1.00[EUR][1000 genomes]
rs6681889	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6694496	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6700225	1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6703115	0.81[AFR][1000 genomes]
rs72908597	1.00[EUR][1000 genomes]
rs7551052	1.00[EUR][1000 genomes]
rs947237	1.00[EUR][1000 genomes]
rs947238	1.00[EUR][1000 genomes]
rs947241	1.00[EUR][1000 genomes]
rs947243	1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs947244	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv870908	chr1:57884310-58037783	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv870802	chr1:57965114-58037031	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr1:57983800-57988400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:57987000-57989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57987200-57987600	Weak transcription	Hela-S3	cervix

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