Variant report

Variant	rs352152
Chromosome Location	chr3:52210700-52210701
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	chr3:52206232..52208818-chr3:52209949..52213336,4	K562	blood:
3	chr3:52208921..52211752-chr3:52239089..52241335,2	MCF-7	breast:
4	chr3:52209128..52211243-chr3:52227235..52228874,2	MCF-7	breast:
5	chr3:52205965..52208673-chr3:52209831..52213095,4	K562	blood:

Variant related genes	Relation type
ENSG00000023330	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12495536	0.93[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs12496447	0.93[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs12629791	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2334961	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28387060	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2878438	0.93[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4687607	0.87[CEU][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs4687805	0.93[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687810	0.93[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6773704	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6777340	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6778442	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6786592	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs731684	0.93[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs735768	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs747343	0.93[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes]
rs749995	0.93[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7644325	0.82[EUR][1000 genomes]
rs876782	0.80[YRI][hapmap]
rs893055	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809254	0.80[YRI][hapmap]
rs9828327	0.93[CEU][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851576	0.93[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs9874939	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	esv3463345	chr3:52210322-52210752	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3463346	chr3:52210322-52210752	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52204800-52215600	Weak transcription	Right Ventricle	heart
2	chr3:52206000-52211000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:52208400-52212800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:52209000-52211000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:52209200-52211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:52209200-52211000	Weak transcription	HMEC	breast
7	chr3:52209200-52211000	Weak transcription	NHLF	lung
8	chr3:52209200-52212000	Enhancers	Spleen	Spleen
9	chr3:52209400-52211200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:52209800-52211600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:52210000-52211000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:52210000-52212200	Enhancers	Esophagus	oesophagus
13	chr3:52210000-52218200	Enhancers	Liver	Liver
14	chr3:52210200-52213200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:52210400-52210800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:52210400-52211600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:52210400-52212000	Enhancers	Gastric	stomach
18	chr3:52210400-52212200	Enhancers	Adipose Nuclei	Adipose
19	chr3:52210400-52212200	Flanking Active TSS	HepG2	liver
20	chr3:52210400-52213200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:52210600-52210800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:52210600-52210800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:52210600-52210800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:52210600-52210800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr3:52210600-52210800	Flanking Active TSS	Hela-S3	cervix
26	chr3:52210600-52211400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:52210600-52211600	Enhancers	Lung	lung
28	chr3:52210600-52211600	Enhancers	NHEK	skin
29	chr3:52210600-52212000	Enhancers	Stomach Mucosa	stomach
30	chr3:52210600-52212600	Enhancers	Fetal Lung	lung

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