Variant report

Variant	rs62262153
Chromosome Location	chr3:105072879-105072880
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	chr3:105072055..105074262-chr3:105075883..105078714,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12497260	0.83[ASN][1000 genomes]
rs13095216	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13095274	0.96[ASN][1000 genomes]
rs1438544	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1438546	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438553	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1438554	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4589964	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55934921	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6437579	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6437582	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6437583	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6437584	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6773531	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6793758	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6797065	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6797259	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6804633	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7611398	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620029	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7620713	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7626665	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7634168	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7635959	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9288801	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9852729	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9869867	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9880342	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9883403	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105068600-105074600	Enhancers	HMEC	breast
2	chr3:105071000-105078200	Weak transcription	A549	lung
3	chr3:105071400-105073200	Weak transcription	NHDF-Ad	bronchial
4	chr3:105071400-105073400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:105071800-105074600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:105072200-105073200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:105072200-105073200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:105072200-105073200	Active TSS	Brain Hippocampus Middle	brain
9	chr3:105072200-105073400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:105072200-105073600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:105072200-105073600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:105072200-105073600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:105072200-105073800	Flanking Active TSS	HUVEC	blood vessel
14	chr3:105072400-105073000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:105072400-105073000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr3:105072400-105073000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
17	chr3:105072400-105073000	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr3:105072400-105073000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr3:105072400-105073000	Active TSS	Gastric	stomach
20	chr3:105072400-105073000	Flanking Active TSS	Pancreas	Pancrea
21	chr3:105072400-105073000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr3:105072400-105073000	Flanking Active TSS	GM12878-XiMat	blood
23	chr3:105072400-105073200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:105072400-105073200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr3:105072400-105073200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:105072400-105073200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:105072400-105073200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:105072400-105073200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr3:105072400-105073200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
30	chr3:105072400-105073200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr3:105072400-105073200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:105072400-105073200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:105072400-105073200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:105072400-105073200	Active TSS	Brain Angular Gyrus	brain
35	chr3:105072400-105073200	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr3:105072400-105073200	Active TSS	Brain Substantia Nigra	brain
37	chr3:105072400-105073200	Active TSS	Colonic Mucosa	Colon
38	chr3:105072400-105073200	Active TSS	Fetal Kidney	kidney
39	chr3:105072400-105073200	Active TSS	Fetal Lung	lung
40	chr3:105072400-105073200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr3:105072400-105073200	Active TSS	HSMM	muscle
42	chr3:105072400-105073200	Flanking Active TSS	NHEK	skin
43	chr3:105072400-105073400	Active TSS	H1 Cell Line	embryonic stem cell
44	chr3:105072400-105073400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr3:105072400-105073400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:105072400-105073400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:105072400-105073400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:105072400-105073400	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr3:105072400-105073400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:105072400-105073400	Active TSS	Brain Anterior Caudate	brain

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