Variant report

Variant	rs7632345
Chromosome Location	chr3:99670983-99670984
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99670705..99673517-chr3:99675233..99678089,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1038295	0.87[ASN][1000 genomes]
rs10804762	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	0.83[ASN][1000 genomes]
rs12486901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs12493124	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[EUR][1000 genomes]
rs12493320	1.00[CEU][hapmap]
rs12494994	0.86[ASW][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs1492343	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1565341	0.84[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap]
rs1871847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590972	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928220	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4928222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4928233	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4928236	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs55874130	0.93[EUR][1000 genomes]
rs55881709	0.89[EUR][1000 genomes]
rs55964918	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140081	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223679	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.90[ASN][1000 genomes]
rs61010376	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440991	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6777622	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6778589	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6792339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.83[ASN][1000 genomes]
rs73860470	0.86[ASN][1000 genomes]
rs7431827	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs7610759	0.86[ASW][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs7614366	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs7634628	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7635633	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7635871	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824430	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs9827744	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs9872339	0.84[CHB][hapmap];0.88[JPT][hapmap]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99663400-99671200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:99664400-99672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:99664400-99672600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:99664400-99672600	Weak transcription	Gastric	stomach
6	chr3:99664400-99674800	Weak transcription	Right Atrium	heart
7	chr3:99664600-99672200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:99664600-99676200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:99664800-99672600	Weak transcription	Left Ventricle	heart
10	chr3:99664800-99672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:99664800-99677200	Weak transcription	Esophagus	oesophagus
12	chr3:99664800-99677200	Weak transcription	Ovary	ovary
13	chr3:99665000-99672400	Weak transcription	Fetal Heart	heart
14	chr3:99665000-99677200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:99665000-99677200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:99665000-99678800	Weak transcription	Aorta	Aorta
17	chr3:99665200-99673800	Weak transcription	Fetal Lung	lung
18	chr3:99665600-99671000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:99666400-99672200	Weak transcription	Psoas Muscle	Psoas
20	chr3:99667800-99671400	Enhancers	HepG2	liver
21	chr3:99667800-99672200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:99669200-99672600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:99669200-99679800	Weak transcription	Fetal Intestine Small	intestine
24	chr3:99669400-99673200	Enhancers	NH-A	brain
25	chr3:99669600-99671400	Enhancers	HSMM	muscle
26	chr3:99669800-99671000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:99669800-99671200	Enhancers	NHLF	lung
28	chr3:99669800-99671800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:99669800-99672800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:99669800-99673000	Enhancers	Osteobl	bone
31	chr3:99669800-99673200	Enhancers	HSMMtube	muscle
32	chr3:99670000-99672600	Weak transcription	Pancreas	Pancrea
33	chr3:99670000-99672800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:99670000-99673000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:99670200-99671400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:99670200-99671400	Enhancers	A549	lung
37	chr3:99670200-99672000	Weak transcription	Stomach Mucosa	stomach
38	chr3:99670200-99672600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:99670200-99672600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:99670400-99671200	Enhancers	HMEC	breast
41	chr3:99670400-99671200	Enhancers	NHDF-Ad	bronchial
42	chr3:99670400-99676000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:99670600-99672000	Weak transcription	K562	blood
44	chr3:99670600-99672600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:99670600-99672600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:99670800-99671200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:99670800-99671200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:99670800-99672000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:99670800-99679200	Weak transcription	Small Intestine	intestine

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