Variant report

Variant	rs10940579
Chromosome Location	chr5:57130818-57130819
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57129335..57131464-chr5:57132447..57134423,2	K562	blood:
2	chr5:57129359..57132461-chr5:57754431..57756056,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12659683	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1835874	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1835875	0.86[AFR][1000 genomes]
rs1968422	0.88[CEU][hapmap];0.90[AMR][1000 genomes]
rs1972768	0.90[AMR][1000 genomes]
rs4323195	0.82[CEU][hapmap];0.90[AMR][1000 genomes]
rs854037	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer (gene x gene interaction)	22219177	GWAS catalog

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57121400-57132800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:57127400-57137400	Enhancers	NHEK	skin
3	chr5:57128400-57132200	Enhancers	HUVEC	blood vessel
4	chr5:57129000-57131000	Weak transcription	NHLF	lung
5	chr5:57129200-57131000	Weak transcription	Lung	lung
6	chr5:57129200-57131000	Weak transcription	Pancreas	Pancrea
7	chr5:57129200-57133800	Weak transcription	Placenta	Placenta
8	chr5:57129200-57136800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:57130200-57131000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:57130200-57136000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:57130200-57139200	Enhancers	HMEC	breast
12	chr5:57130400-57131000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:57130400-57131400	Enhancers	Hela-S3	cervix
14	chr5:57130400-57132200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:57130400-57132200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:57130600-57131200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:57130600-57131600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr5:57130600-57131600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:57130600-57131600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:57130600-57131600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr5:57130600-57131600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:57130600-57131600	Enhancers	A549	lung
23	chr5:57130600-57131600	Enhancers	NH-A	brain
24	chr5:57130600-57131800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr5:57130600-57132000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:57130600-57132200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr5:57130600-57132200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr5:57130600-57132600	Enhancers	HSMMtube	muscle
29	chr5:57130600-57134800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr5:57130600-57137800	Enhancers	HSMM	muscle
31	chr5:57130800-57131200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:57130800-57131200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:57130800-57131400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr5:57130800-57131400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:57130800-57131400	Enhancers	Colon Smooth Muscle	Colon
36	chr5:57130800-57131400	Enhancers	Fetal Muscle Trunk	muscle
37	chr5:57130800-57131400	Enhancers	Stomach Mucosa	stomach
38	chr5:57130800-57131600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr5:57130800-57131600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:57130800-57131600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:57130800-57131600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:57130800-57131600	Enhancers	Fetal Muscle Leg	muscle
43	chr5:57130800-57131600	Enhancers	Fetal Stomach	stomach
44	chr5:57130800-57131600	Enhancers	HepG2	liver
45	chr5:57130800-57131600	Enhancers	NHDF-Ad	bronchial
46	chr5:57130800-57132000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr5:57130800-57132200	Enhancers	Osteobl	bone
48	chr5:57130800-57132400	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links