Variant report

Variant	rs62256009
Chromosome Location	chr3:53296563-53296564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53288022..53293175-chr3:53295938..53300780,7	MCF-7	breast:
2	chr3:53296022..53298789-chr3:53302233..53304296,2	K562	blood:

Variant related genes	Relation type
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10433617	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433618	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108506	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030934	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17234771	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235667	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41275543	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56654807	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59145995	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255993	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255994	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255999	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256000	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256003	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256043	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256049	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256050	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256053	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256965	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256966	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256968	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256969	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257004	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62257007	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62257009	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257011	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257013	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62257024	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6780100	0.89[EUR][1000 genomes]
rs73080266	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73082274	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7622159	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830594	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830895	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846315	0.95[EUR][1000 genomes]
rs9850440	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864057	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53292600-53298000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:53293000-53297400	Enhancers	HMEC	breast
3	chr3:53293400-53296600	Enhancers	Adipose Nuclei	Adipose
4	chr3:53294000-53303600	Weak transcription	HSMMtube	muscle
5	chr3:53294200-53298600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:53294200-53298600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:53294200-53298800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:53294200-53299200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:53294200-53300000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:53294200-53303600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:53294200-53303800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:53294400-53298400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:53294400-53298400	Weak transcription	Right Ventricle	heart
14	chr3:53294400-53298600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:53294400-53298800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:53294400-53300200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:53294600-53298800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:53294600-53298800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:53294600-53300200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:53294600-53302000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:53294600-53303400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:53294600-53303400	Weak transcription	Brain Substantia Nigra	brain
23	chr3:53294600-53303600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:53294600-53303600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:53294600-53304000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:53294600-53304200	Weak transcription	Lung	lung
27	chr3:53294800-53297000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:53294800-53297400	Enhancers	NHEK	skin
29	chr3:53294800-53298400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:53294800-53304000	Weak transcription	Psoas Muscle	Psoas
31	chr3:53295000-53298600	Weak transcription	Fetal Heart	heart
32	chr3:53295000-53298600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:53296000-53298800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:53296000-53298800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:53296000-53299600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:53296000-53303600	Weak transcription	Gastric	stomach
37	chr3:53296000-53303800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:53296200-53298200	Weak transcription	Hela-S3	cervix
39	chr3:53296200-53298400	Weak transcription	Left Ventricle	heart
40	chr3:53296200-53298800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:53296200-53299000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:53296200-53299000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:53296200-53302200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:53296200-53303000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:53296200-53303600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:53296200-53303600	Weak transcription	Esophagus	oesophagus
47	chr3:53296200-53303600	Weak transcription	NHDF-Ad	bronchial
48	chr3:53296200-53304000	Weak transcription	Right Atrium	heart
49	chr3:53296400-53296600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr3:53296400-53297200	Enhancers	Primary neutrophils fromperipheralblood	blood

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