Variant report

Variant	rs2925176
Chromosome Location	chr5:114686388-114686389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114679467..114681719-chr5:114684783..114686462,2	MCF-7	breast:
2	chr5:114684315..114686804-chr5:114699761..114703151,3	MCF-7	breast:
3	chr5:114684923..114687341-chr5:114688563..114690292,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10057172	1.00[JPT][hapmap]
rs10478230	0.85[CEU][hapmap]
rs10478231	0.85[CEU][hapmap]
rs2004680	0.85[CEU][hapmap]
rs2605185	0.82[CEU][hapmap]
rs28433223	0.93[ASN][1000 genomes]
rs2925175	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2925176	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114684400-114688000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:114684600-114687800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:114684600-114688000	Enhancers	Hela-S3	cervix
4	chr5:114684800-114687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:114685400-114686400	Enhancers	Ovary	ovary
6	chr5:114685400-114686600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:114685400-114691400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:114685600-114686600	Weak transcription	K562	blood
9	chr5:114685600-114687400	Enhancers	A549	lung
10	chr5:114685600-114688200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:114685600-114695800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:114685800-114687000	Weak transcription	HUVEC	blood vessel
13	chr5:114685800-114687200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:114685800-114687400	Weak transcription	NH-A	brain
15	chr5:114685800-114688000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr5:114685800-114689600	Weak transcription	Liver	Liver
17	chr5:114686000-114686400	Enhancers	Pancreas	Pancrea
18	chr5:114686000-114686400	Enhancers	Stomach Mucosa	stomach
19	chr5:114686000-114687000	Weak transcription	Osteobl	bone
20	chr5:114686000-114687200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:114686000-114687200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:114686000-114687200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:114686000-114687200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:114686000-114687200	Weak transcription	Brain Substantia Nigra	brain
25	chr5:114686000-114687200	Weak transcription	NHEK	skin
26	chr5:114686000-114687200	Weak transcription	NHLF	lung
27	chr5:114686000-114687400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:114686000-114687400	Weak transcription	HMEC	breast
29	chr5:114686000-114687600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:114686200-114687200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:114686200-114687200	Weak transcription	NHDF-Ad	bronchial
32	chr5:114686200-114687400	Weak transcription	HSMM	muscle
33	chr5:114686200-114687400	Weak transcription	HSMMtube	muscle
34	chr5:114686200-114689600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links