Variant report

Variant	rs62370279
Chromosome Location	chr5:53075810-53075811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr5:53075567-53075858	SK-N-SH	brain:	n/a	n/a
2	JUN	chr5:53075536-53075848	HUVEC	blood vessel:	n/a	chr5:53075692-53075703
3	FOS	chr5:53075626-53075882	MCF10A-Er-Src	breast:	n/a	chr5:53075692-53075703
4	STAT3	chr5:53075543-53075886	MCF10A-Er-Src	breast:	n/a	chr5:53075696-53075708
5	STAT3	chr5:53075548-53075951	MCF10A-Er-Src	breast:	n/a	chr5:53075696-53075708
6	EP300	chr5:53075467-53075855	SK-N-SH_RA	brain:	n/a	chr5:53075699-53075712
7	NFIC	chr5:53075089-53076059	SK-N-SH	brain:	n/a	chr5:53075422-53075450
8	FOS	chr5:53075570-53075826	MCF10A-Er-Src	breast:	n/a	chr5:53075692-53075703
9	EP300	chr5:53075289-53075817	SK-N-SH_RA	brain:	n/a	chr5:53075699-53075712
10	FOS	chr5:53075308-53075960	HUVEC	blood vessel:	n/a	chr5:53075692-53075703
11	CEBPB	chr5:53075450-53075832	IMR90	lung:	n/a	n/a
12	STAT3	chr5:53075543-53075947	MCF10A-Er-Src	breast:	n/a	chr5:53075696-53075708
13	POLR2A	chr5:53075435-53075884	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr5:53075365-53075848	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:53074472..53076852-chr5:53081313..53084194,2	MCF-7	breast:
2	chr5:53072410..53076632-chr5:53077579..53083157,6	K562	blood:

Variant related genes	Relation type
ENSG00000263710	TF binding region
ENSG00000263710	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11953900	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11955732	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17307165	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2124949	0.80[AMR][1000 genomes]
rs4147737	0.82[AMR][1000 genomes]
rs4147738	0.80[AMR][1000 genomes]
rs4147743	0.84[AMR][1000 genomes]
rs56099109	0.84[AMR][1000 genomes]
rs62370277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv830298	chr5:52973912-53193398	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 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	chr5:53073600-53076200	Enhancers	Stomach Mucosa	stomach
2	chr5:53073800-53076000	Enhancers	GM12878-XiMat	blood
3	chr5:53073800-53076400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:53074200-53076200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:53074200-53076400	Enhancers	HSMM	muscle
6	chr5:53074400-53076200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:53074400-53076200	Enhancers	NHEK	skin
8	chr5:53074400-53076400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:53074600-53076000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:53074800-53076000	Enhancers	Fetal Stomach	stomach
11	chr5:53074800-53076000	Enhancers	HepG2	liver
12	chr5:53074800-53076200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:53074800-53076200	Enhancers	NHDF-Ad	bronchial
14	chr5:53074800-53076400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:53075000-53076000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:53075000-53076200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr5:53075000-53076200	Enhancers	HMEC	breast
18	chr5:53075000-53076200	Enhancers	HUVEC	blood vessel
19	chr5:53075000-53076200	Enhancers	NHLF	lung
20	chr5:53075200-53076000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:53075200-53076000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:53075200-53076200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:53075200-53076200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:53075200-53076200	Flanking Active TSS	HSMMtube	muscle
25	chr5:53075400-53076000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr5:53075400-53076200	Enhancers	Dnd41	blood
27	chr5:53075400-53076200	Enhancers	NH-A	brain
28	chr5:53075600-53076200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:53075600-53078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:53075600-53086000	Weak transcription	Pancreas	Pancrea
31	chr5:53075800-53076000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:53075800-53076200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:53075800-53076200	Enhancers	Osteobl	bone
34	chr5:53075800-53078400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:53075800-53079200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links