Variant report

Variant	rs2939534
Chromosome Location	chr5:145564980-145564981
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:145564834-145565101	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr5:145564823-145565032	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr5:145564868-145564982	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr5:145564778-145565046	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr5:145564742-145565108	HUVEC	blood vessel:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:145562850..145566563-chr5:145571128..145574037,3	MCF-7	breast:
2	chr5:145564650..145566770-chr5:145588134..145589874,2	K562	blood:
3	chr5:145564948..145567866-chr5:145592052..145594140,2	K562	blood:
4	chr5:145563092..145566274-chr5:145579879..145584548,5	MCF-7	breast:
5	chr5:145560592..145565120-chr5:145580444..145584486,7	K562	blood:

No data

Variant related genes	Relation type
LARS	TF binding region
ENSG00000091009	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10491259	0.91[YRI][hapmap]
rs11953506	0.80[YRI][hapmap]
rs11960075	0.80[YRI][hapmap]
rs2063002	0.91[YRI][hapmap]
rs2939522	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2939526	1.00[AMR][1000 genomes]
rs2939536	0.91[YRI][hapmap]
rs2939537	0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2939538	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962500	1.00[YRI][hapmap]
rs2962505	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2962506	0.80[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962507	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962512	0.80[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962513	0.96[AFR][1000 genomes]
rs2962514	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962516	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963913	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963937	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4705440	0.88[AFR][1000 genomes]
rs6877277	0.91[YRI][hapmap]
rs7707229	0.91[YRI][hapmap]

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	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428128	chr5:145503978-145682880	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv883007	chr5:145506100-145672431	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv883008	chr5:145509728-145642925	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3348501	chr5:145543808-145572250	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145562800-145569800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:145563000-145565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:145563000-145568000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:145563000-145568800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:145563000-145582200	Weak transcription	Right Atrium	heart
6	chr5:145563400-145566800	Weak transcription	Placenta	Placenta
7	chr5:145563400-145570600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:145564600-145565000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:145564600-145565000	Enhancers	A549	lung
10	chr5:145564600-145565000	Enhancers	NHDF-Ad	bronchial
11	chr5:145564600-145565200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:145564600-145565200	Enhancers	HMEC	breast
13	chr5:145564600-145565200	Enhancers	HUVEC	blood vessel
14	chr5:145564600-145565200	Enhancers	Osteobl	bone
15	chr5:145564600-145565400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:145564600-145565400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:145564600-145565400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:145564600-145565400	Enhancers	NHEK	skin
19	chr5:145564800-145565200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr5:145564800-145565200	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links