Variant report

Variant	rs4539980
Chromosome Location	chr3:142450799-142450800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142449190..142450946-chr3:142453466..142455123,2	K562	blood:
2	chr3:142440764..142447351-chr3:142447876..142453458,13	K562	blood:
3	chr3:142450124..142452703-chr3:142455616..142457885,2	K562	blood:
4	chr3:142446381..142451042-chr3:142452461..142456745,6	MCF-7	breast:
5	chr3:142429711..142432436-chr3:142449677..142451639,2	K562	blood:

Variant related genes	Relation type
ENSG00000144935	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11715459	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11915805	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1382688	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs1604	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1871349	0.95[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2033912	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2177398	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs28571594	0.86[AMR][1000 genomes]
rs28689551	0.89[ASN][1000 genomes]
rs35467195	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35862982	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3844273	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4643748	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs55722917	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56775607	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59108985	0.89[ASN][1000 genomes]
rs6440104	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs6440106	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440108	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6440110	0.87[ASN][1000 genomes]
rs6772222	0.89[ASN][1000 genomes]
rs6784998	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6790959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6803681	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7621642	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7623762	0.86[AMR][1000 genomes]
rs7626908	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7628728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629129	0.83[AMR][1000 genomes]
rs7637846	0.86[YRI][hapmap]
rs7638459	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7639403	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7644704	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653309	0.89[ASN][1000 genomes]
rs953239	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9754885	0.80[ASN][1000 genomes]
rs9820721	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9823836	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9824476	0.89[ASN][1000 genomes]
rs9835135	0.88[ASN][1000 genomes]
rs9836269	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9849461	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9851381	0.95[CHB][hapmap]
rs9861598	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9864230	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9865053	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142444000-142452600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:142444200-142467400	Weak transcription	HSMM	muscle
3	chr3:142444400-142451000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:142444400-142451200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:142444400-142454400	Weak transcription	Ovary	ovary
6	chr3:142444400-142467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:142444400-142469600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:142444600-142451200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:142444600-142453800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:142444600-142454200	Weak transcription	NHLF	lung
11	chr3:142444600-142467200	Weak transcription	NH-A	brain
12	chr3:142445000-142451000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:142445000-142451200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:142445000-142467400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:142445000-142467800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:142445000-142479000	Weak transcription	Fetal Brain Female	brain
17	chr3:142445200-142450800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:142445200-142451000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:142445200-142467000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:142445200-142467000	Weak transcription	NHDF-Ad	bronchial
21	chr3:142445200-142467000	Weak transcription	Osteobl	bone
22	chr3:142445200-142467200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:142445200-142467400	Weak transcription	HMEC	breast
24	chr3:142445400-142467200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:142445800-142467400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:142446000-142467000	Weak transcription	A549	lung
27	chr3:142446400-142467200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:142446800-142450800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:142448400-142455200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:142449800-142454200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:142450000-142454000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:142450200-142467000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:142450400-142451000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:142450600-142451400	Enhancers	HepG2	liver
35	chr3:142450600-142451600	Enhancers	HUES48 Cell Line	embryonic stem cell

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