Variant report

Variant	rs352149
Chromosome Location	chr3:52209530-52209531
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52209175..52211275-chr3:52220260..52222070,2	K562	blood:
2	chr3:52208199..52210060-chr3:52231169..52233721,2	MCF-7	breast:
3	chr3:52205020..52207275-chr3:52207842..52209830,2	MCF-7	breast:
4	chr3:52208921..52211752-chr3:52239089..52241335,2	MCF-7	breast:
5	chr3:52205035..52206671-chr3:52208297..52209817,2	K562	blood:
6	chr3:52006199..52007889-chr3:52209078..52210620,2	K562	blood:
7	chr3:52209128..52211243-chr3:52227235..52228874,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248487	Chromatin interaction
ENSG00000023330	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs123681	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386365	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13314125	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13319566	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs164638	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051957	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs17051977	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs171294	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs183029	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304505	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28452586	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28659792	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352146	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352147	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352150	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352153	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55664415	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55834589	0.86[EUR][1000 genomes]
rs56281986	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56322622	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57335685	0.89[EUR][1000 genomes]
rs57466127	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59890038	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6781635	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72964042	0.84[EUR][1000 genomes]
rs72964044	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7638246	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs808787	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs876782	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs893056	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9809254	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9809977	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9811707	0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815010	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9816434	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817653	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830293	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841469	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843299	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843852	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9847073	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847092	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9857878	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs9860982	0.89[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9868101	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9882775	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52196200-52210400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:52204800-52215600	Weak transcription	Right Ventricle	heart
3	chr3:52205400-52210200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:52206000-52211000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:52206200-52210400	Weak transcription	Gastric	stomach
6	chr3:52206200-52210600	Weak transcription	Stomach Mucosa	stomach
7	chr3:52207600-52210400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:52208400-52209800	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr3:52208400-52212800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:52208600-52209800	Enhancers	HepG2	liver
11	chr3:52208800-52209600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52208800-52209600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:52208800-52209800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:52209000-52209600	Enhancers	Esophagus	oesophagus
15	chr3:52209000-52210600	Weak transcription	NHEK	skin
16	chr3:52209000-52211000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:52209200-52211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:52209200-52211000	Weak transcription	HMEC	breast
19	chr3:52209200-52211000	Weak transcription	NHLF	lung
20	chr3:52209200-52212000	Enhancers	Spleen	Spleen
21	chr3:52209400-52210600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:52209400-52210600	Weak transcription	Hela-S3	cervix
23	chr3:52209400-52211200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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