Variant report

Variant	rs12520199
Chromosome Location	chr5:127006289-127006290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10060515	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10463500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10463830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10463831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10519957	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11241937	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12109863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12110005	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12513657	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12513840	0.81[ASN][1000 genomes]
rs12514061	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12514063	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12515664	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12515942	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12516808	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12518298	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12522171	0.92[ASN][1000 genomes]
rs12522308	0.81[ASN][1000 genomes]
rs17696654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17696713	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17696737	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17764290	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17764334	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17764418	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2280170	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835929	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4836329	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4836331	0.81[ASN][1000 genomes]
rs4836333	0.81[ASN][1000 genomes]
rs6860127	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6874681	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6874932	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6877039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73341170	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73341185	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73343005	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73343059	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7707416	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7722425	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7734486	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9686108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv830479	chr5:126849254-127053121	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv599664	chr5:126974071-127016256	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126996400-127006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:127002800-127022200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:127003600-127009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:127006200-127006400	Enhancers	Stomach Smooth Muscle	stomach

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