Variant report

Variant	rs1549562
Chromosome Location	chr12:40790940-40790941
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1035812	0.83[JPT][hapmap]
rs1035813	0.84[JPT][hapmap]
rs10748040	0.84[JPT][hapmap]
rs10784518	0.83[JPT][hapmap]
rs10784528	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs10784536	0.84[JPT][hapmap]
rs10784587	0.95[ASN][1000 genomes]
rs11564230	0.84[JPT][hapmap];0.84[YRI][hapmap]
rs1365763	0.84[JPT][hapmap]
rs1365765	0.84[JPT][hapmap]
rs1365766	0.84[JPT][hapmap]
rs1427259	1.00[CEU][hapmap];1.00[CHB][hapmap];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]
rs1427261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427271	0.84[JPT][hapmap]
rs1427272	0.84[JPT][hapmap]
rs1427273	0.84[JPT][hapmap]
rs1465527	0.82[EUR][1000 genomes]
rs1816207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1822606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834745	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1834746	0.86[ASN][1000 genomes]
rs2081702	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2217148	0.95[ASN][1000 genomes]
rs2404836	0.84[JPT][hapmap]
rs3789330	0.83[JPT][hapmap]
rs3861083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3943893	0.84[JPT][hapmap]
rs4099579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4465428	0.90[CEU][hapmap]
rs4473003	0.88[CEU][hapmap]
rs4767971	0.82[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs4767972	0.83[JPT][hapmap]
rs4767974	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4767975	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4768232	0.84[JPT][hapmap]
rs4768234	0.84[JPT][hapmap]
rs4768235	0.84[JPT][hapmap]
rs4768238	0.83[EUR][1000 genomes]
rs4768250	0.95[ASN][1000 genomes]
rs6581723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7131694	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs7134572	0.90[CEU][hapmap]
rs7136122	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs7137437	0.84[JPT][hapmap]
rs715402	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs7294952	0.84[JPT][hapmap]
rs7294958	0.84[JPT][hapmap]
rs7306545	0.84[JPT][hapmap]
rs7307310	0.88[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs7308626	0.83[JPT][hapmap]
rs7311247	0.84[JPT][hapmap]
rs7313525	0.84[JPT][hapmap]
rs7313895	0.84[JPT][hapmap]
rs7314455	0.83[JPT][hapmap]
rs7314863	0.84[JPT][hapmap]
rs7954061	0.84[JPT][hapmap]
rs7955042	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7955308	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7956787	0.84[JPT][hapmap]
rs7956898	0.84[JPT][hapmap]
rs7957151	0.84[JPT][hapmap]
rs7959481	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7962116	0.84[JPT][hapmap]
rs7962370	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs7963086	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs7963987	0.84[JPT][hapmap]
rs7966143	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971919	0.84[JPT][hapmap]
rs7976724	0.84[JPT][hapmap]
rs890575	0.84[JPT][hapmap]
rs919175	0.84[JPT][hapmap]

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	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv899032	chr12:40735939-40827479	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv558598	chr12:40742363-40828264	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1047639	chr12:40774370-40804386	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv558599	chr12:40790698-40814452	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40787200-40799200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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