Variant report

Variant	rs1920661
Chromosome Location	chr3:160288537-160288538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160156708..160158312-chr3:160288090..160290046,2	K562	blood:
2	chr3:160281906..160285341-chr3:160285654..160289811,8	MCF-7	breast:
3	chr3:160287495..160289317-chr3:160290381..160292497,2	MCF-7	breast:
4	chr3:160282613..160284767-chr3:160285868..160288833,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10212356	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11919703	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13314803	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16831286	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs16831313	0.87[EUR][1000 genomes]
rs2178454	0.87[EUR][1000 genomes]
rs28631610	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55804574	0.87[EUR][1000 genomes]
rs6441326	0.87[EUR][1000 genomes]
rs6778401	0.93[EUR][1000 genomes]
rs6778711	0.93[EUR][1000 genomes]
rs9813697	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap]
rs9825299	0.86[EUR][1000 genomes]
rs9829578	0.86[EUR][1000 genomes]
rs9838380	0.87[EUR][1000 genomes]
rs9843737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs9847211	0.82[EUR][1000 genomes]
rs9857038	0.87[EUR][1000 genomes]
rs9857327	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9874550	1.00[CEU][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
5	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers 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	49 gene(s)	inside rSNPs	diseases
6	nsv4089	chr3:160284848-160330024	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160284200-160289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:160284800-160289600	Weak transcription	Fetal Lung	lung
3	chr3:160284800-160292000	Weak transcription	Brain Anterior Caudate	brain
4	chr3:160284800-160295000	Weak transcription	Stomach Mucosa	stomach
5	chr3:160284800-160295200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:160285000-160289600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:160285000-160290800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:160285000-160292200	Weak transcription	Primary B cells from cord blood	blood
9	chr3:160285200-160289600	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:160285200-160293400	Weak transcription	HepG2	liver
11	chr3:160285200-160294400	Weak transcription	HSMMtube	muscle
12	chr3:160285200-160298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:160285600-160289200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:160285800-160288800	Weak transcription	NHEK	skin
15	chr3:160285800-160290800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:160286600-160288600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:160286600-160288600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:160286800-160288800	Weak transcription	NHLF	lung
19	chr3:160286800-160289200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:160286800-160289800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:160286800-160290400	Weak transcription	Right Ventricle	heart
22	chr3:160286800-160291200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:160286800-160292800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:160286800-160294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:160286800-160295600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:160286800-160295800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:160286800-160301200	Weak transcription	HMEC	breast
28	chr3:160287000-160288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:160287000-160288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:160287000-160288600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr3:160287000-160288800	Weak transcription	Pancreas	Pancrea
32	chr3:160287000-160288800	Weak transcription	A549	lung
33	chr3:160287000-160289200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:160287000-160289200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:160287000-160289600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:160287000-160292000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:160287000-160292000	Weak transcription	Gastric	stomach
38	chr3:160287000-160293600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:160287000-160295600	Weak transcription	Adipose Nuclei	Adipose
40	chr3:160287200-160289600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:160287200-160290000	Weak transcription	Fetal Intestine Small	intestine
42	chr3:160287200-160291800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:160287400-160291800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:160287800-160288600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr3:160288000-160295400	Weak transcription	Psoas Muscle	Psoas
46	chr3:160288000-160295600	Weak transcription	Liver	Liver
47	chr3:160288200-160295600	Weak transcription	Muscle Satellite Cultured Cells	--

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