Variant report

Variant	rs1546421
Chromosome Location	chr3:146276275-146276276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1057481	1.00[JPT][hapmap]
rs1061307	0.89[CHB][hapmap]
rs1079369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13064509	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13069082	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13074501	0.96[CEU][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099587	0.89[CHB][hapmap]
rs1373246	1.00[JPT][hapmap]
rs1443827	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1546420	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579786	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1579787	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16858420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1882972	1.00[JPT][hapmap]
rs1882973	1.00[JPT][hapmap]
rs1882974	1.00[JPT][hapmap]
rs1997604	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2083866	0.97[ASN][1000 genomes]
rs2120381	0.93[JPT][hapmap]
rs2165948	1.00[JPT][hapmap]
rs2587008	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2587011	1.00[JPT][hapmap]
rs2587012	1.00[JPT][hapmap]
rs2587013	1.00[JPT][hapmap]
rs2587014	1.00[JPT][hapmap]
rs2587015	1.00[JPT][hapmap]
rs2587016	0.94[JPT][hapmap]
rs2587017	1.00[JPT][hapmap]
rs2587018	1.00[JPT][hapmap]
rs2587021	0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2587023	1.00[JPT][hapmap]
rs2587024	0.94[JPT][hapmap]
rs2609860	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2609861	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2609864	1.00[JPT][hapmap]
rs2609865	1.00[JPT][hapmap]
rs2609866	1.00[JPT][hapmap]
rs2688688	0.94[JPT][hapmap]
rs2738906	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2738907	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2738910	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2738911	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2738915	1.00[JPT][hapmap]
rs2738916	1.00[JPT][hapmap]
rs2738918	1.00[JPT][hapmap]
rs2738920	1.00[JPT][hapmap]
rs2738921	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2738923	1.00[JPT][hapmap]
rs34682680	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35046242	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35416584	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7639636	0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9289722	1.00[JPT][hapmap]
rs977757	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977758	0.90[EUR][1000 genomes]
rs977759	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810169	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813199	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs9832220	0.96[CEU][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833135	0.96[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850802	0.89[CHB][hapmap]
rs9861142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9865918	0.90[EUR][1000 genomes]
rs9876886	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
2	nsv432489	chr3:146271370-146323969	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146270000-146284000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:146275200-146276400	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr3:146275400-146277400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:146275400-146277400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:146275600-146277600	Enhancers	Primary B cells from cord blood	blood
6	chr3:146275800-146276600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:146275800-146286200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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