Variant report

Variant	rs1443827
Chromosome Location	chr3:146273572-146273573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146254083..146256051-chr3:146272994..146275921,2	MCF-7	breast:
2	chr3:146259917..146263549-chr3:146271246..146274873,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1057481	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1061307	0.89[CHB][hapmap]
rs1079369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13064509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13069082	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13074501	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs13099587	0.89[CHB][hapmap]
rs1373246	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1546420	0.90[EUR][1000 genomes]
rs1546421	0.90[EUR][1000 genomes]
rs1579786	0.88[EUR][1000 genomes]
rs1579787	0.88[EUR][1000 genomes]
rs16858420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1882971	0.86[ASN][1000 genomes]
rs1882972	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1882973	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1882974	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1997601	0.87[ASN][1000 genomes]
rs1997604	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2120381	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2165948	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587007	0.87[ASN][1000 genomes]
rs2587008	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2587009	0.87[ASN][1000 genomes]
rs2587010	0.86[ASN][1000 genomes]
rs2587011	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587012	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587013	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587014	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587015	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587016	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587017	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587018	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2587021	0.82[JPT][hapmap]
rs2587023	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2587024	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2609858	0.94[ASN][1000 genomes]
rs2609860	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2609861	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2609862	0.86[ASN][1000 genomes]
rs2609864	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2609865	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2609866	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2609867	0.86[ASN][1000 genomes]
rs2688688	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2738905	0.85[ASN][1000 genomes]
rs2738906	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2738907	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2738910	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2738911	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2738912	0.87[ASN][1000 genomes]
rs2738915	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2738916	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2738918	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2738920	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2738921	0.82[JPT][hapmap]
rs2738923	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34682680	0.83[EUR][1000 genomes]
rs35046242	0.90[EUR][1000 genomes]
rs35214899	0.93[ASN][1000 genomes]
rs35309521	0.90[ASN][1000 genomes]
rs35416584	0.88[EUR][1000 genomes]
rs3773510	0.86[ASN][1000 genomes]
rs67703040	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7615988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289722	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs977757	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs977758	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977759	0.90[EUR][1000 genomes]
rs9810169	0.88[EUR][1000 genomes]
rs9832220	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs9833135	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs9850802	0.89[CHB][hapmap]
rs9861142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865918	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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:11 , 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	chr3:146270200-146274200	Weak transcription	HMEC	breast
3	chr3:146272200-146275600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:146272400-146275600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:146272600-146275200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:146272600-146275400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:146272600-146275400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:146272600-146275400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:146272800-146274600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:146273200-146273600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:146273200-146274000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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