Variant report

Variant	rs56942787
Chromosome Location	chr5:57555809-57555810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:57550054..57551732-chr5:57553774..57557457,3	K562	blood:
2	chr5:57531620..57533585-chr5:57553744..57556130,2	MCF-7	breast:
3	chr5:57482131..57485678-chr5:57554046..57557182,5	MCF-7	breast:
4	chr5:57546757..57549531-chr5:57552284..57556177,4	MCF-7	breast:
5	chr5:57551727..57557881-chr5:57751726..57757187,9	MCF-7	breast:
6	chr5:57553683..57556320-chr5:57556923..57559469,3	MCF-7	breast:
7	chr5:57553536..57556295-chr5:57753554..57756650,6	MCF-7	breast:
8	chr5:57555431..57557265-chr5:57747866..57749684,2	MCF-7	breast:
9	chr5:57554637..57557710-chr5:57746924..57749357,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

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

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

rs_ID	r²[population]
rs10045556	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10076155	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187672	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188902	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658947	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12659412	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1477347	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs151865	0.89[ASN][1000 genomes]
rs151870	0.89[ASN][1000 genomes]
rs151872	0.95[ASN][1000 genomes]
rs151873	0.95[ASN][1000 genomes]
rs151874	0.95[ASN][1000 genomes]
rs151875	0.95[ASN][1000 genomes]
rs151876	0.95[ASN][1000 genomes]
rs151877	0.95[ASN][1000 genomes]
rs151878	0.95[ASN][1000 genomes]
rs17695268	0.86[EUR][1000 genomes]
rs17696032	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052548	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2409008	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5868101	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68192123	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858896	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892109	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72755727	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72755734	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72755740	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72755746	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72755747	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[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	esv3489100	chr5:57545689-57669673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3489101	chr5:57545689-57669673	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57552600-57557400	Weak transcription	Aorta	Aorta
2	chr5:57553800-57556400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr5:57554200-57556600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:57554400-57556800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:57554400-57557800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:57554600-57556000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:57554800-57556000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:57554800-57556200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr5:57555000-57556200	Flanking Active TSS	HMEC	breast
10	chr5:57555000-57556600	Enhancers	NHDF-Ad	bronchial
11	chr5:57555200-57556000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:57555200-57556000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr5:57555200-57556000	Enhancers	Fetal Muscle Leg	muscle
14	chr5:57555200-57556000	Enhancers	Left Ventricle	heart
15	chr5:57555200-57556000	Flanking Active TSS	HUVEC	blood vessel
16	chr5:57555200-57556000	Flanking Active TSS	NHEK	skin
17	chr5:57555200-57556200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:57555200-57556200	Flanking Active TSS	Hela-S3	cervix
19	chr5:57555200-57556200	Flanking Active TSS	Osteobl	bone
20	chr5:57555200-57556400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:57555200-57556400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr5:57555200-57556400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr5:57555400-57556200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr5:57555400-57556200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:57555400-57556200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:57555400-57556200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:57555400-57556200	Enhancers	HSMMtube	muscle
28	chr5:57555400-57556200	Flanking Active TSS	NH-A	brain
29	chr5:57555600-57556000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:57555600-57556000	Enhancers	Placenta	Placenta
31	chr5:57555600-57556000	Enhancers	Ovary	ovary
32	chr5:57555600-57556000	Enhancers	Right Atrium	heart
33	chr5:57555600-57556000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr5:57555600-57556000	Active TSS	A549	lung
35	chr5:57555600-57556000	Flanking Active TSS	HSMM	muscle
36	chr5:57555600-57556000	Flanking Active TSS	NHLF	lung
37	chr5:57555600-57556200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:57555600-57556200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:57555600-57556200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr5:57555600-57556200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:57555600-57557000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:57555600-57558000	Enhancers	Fetal Heart	heart
43	chr5:57555800-57556000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr5:57555800-57556000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:57555800-57556000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr5:57555800-57556000	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr5:57555800-57556000	Enhancers	Fetal Lung	lung
48	chr5:57555800-57556000	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr5:57555800-57556200	Enhancers	H9 Cell Line	embryonic stem cell
50	chr5:57555800-57556400	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links