Variant report

Variant	rs62278494
Chromosome Location	chr3:142445688-142445689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142443679..142445893-chr3:142461230..142463554,2	K562	blood:
2	chr3:142442816..142444880-chr3:142445046..142446610,2	K562	blood:
3	chr3:142443512..142446497-chr3:142575988..142578278,2	K562	blood:
4	chr3:142296594..142299227-chr3:142445379..142447905,3	K562	blood:
5	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:

Variant related genes	Relation type
ENSG00000120756	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000144935	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10935467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11915810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11929069	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13081200	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13081255	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13087943	0.86[AFR][1000 genomes]
rs13092601	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13094259	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17624218	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1916638	0.86[AFR][1000 genomes]
rs34084493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34485065	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs36085850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55968753	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62278490	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62278492	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62278493	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62278495	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62278498	0.87[AMR][1000 genomes];0.91[EUR][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:40 , 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	chr3:142444400-142446400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:142444400-142451000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:142444400-142451200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:142444400-142454400	Weak transcription	Ovary	ovary
7	chr3:142444400-142467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:142444400-142469600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:142444600-142445800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:142444600-142445800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:142444600-142446000	Enhancers	Brain Cingulate Gyrus	brain
12	chr3:142444600-142446200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:142444600-142451200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:142444600-142453800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:142444600-142454200	Weak transcription	NHLF	lung
16	chr3:142444600-142467200	Weak transcription	NH-A	brain
17	chr3:142445000-142446000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:142445000-142446200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:142445000-142446400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:142445000-142446400	Enhancers	HepG2	liver
21	chr3:142445000-142451000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:142445000-142451200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:142445000-142467400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:142445000-142467800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:142445000-142479000	Weak transcription	Fetal Brain Female	brain
26	chr3:142445200-142445800	Enhancers	K562	blood
27	chr3:142445200-142446000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:142445200-142447800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:142445200-142449000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:142445200-142450800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:142445200-142451000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:142445200-142467000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:142445200-142467000	Weak transcription	NHDF-Ad	bronchial
34	chr3:142445200-142467000	Weak transcription	Osteobl	bone
35	chr3:142445200-142467200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:142445200-142467400	Weak transcription	HMEC	breast
37	chr3:142445400-142445800	Weak transcription	A549	lung
38	chr3:142445400-142467200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:142445600-142446000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:142445600-142450600	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links