Variant report

Variant	rs10489273
Chromosome Location	chr1:172940607-172940608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172940580..172943092-chr1:173158852..173161378,2	K562	blood:

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10912505	0.92[EUR][1000 genomes]
rs2143183	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2179424	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[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	nsv831904	chr1:172912110-173070429	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv533953	chr1:172939335-173133255	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489273	CD247	cis	cerebellum	SCAN
rs10489273	FMO4	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172936000-172941200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:172936200-172944800	Weak transcription	Stomach Mucosa	stomach
3	chr1:172936400-172941800	Enhancers	NHDF-Ad	bronchial
4	chr1:172937200-172941000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:172938200-172941800	Enhancers	HSMMtube	muscle
6	chr1:172938600-172940800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:172938600-172941200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:172938800-172940800	Enhancers	NH-A	brain
9	chr1:172938800-172941600	Enhancers	Placenta	Placenta
10	chr1:172938800-172941600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:172938800-172941800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:172938800-172942000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:172938800-172942800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:172938800-172943200	Enhancers	HMEC	breast
15	chr1:172938800-172943200	Enhancers	NHEK	skin
16	chr1:172939200-172942000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:172939200-172944600	Weak transcription	HepG2	liver
18	chr1:172939400-172942400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:172939600-172941600	Enhancers	Pancreas	Pancrea
20	chr1:172939600-172941600	Enhancers	A549	lung
21	chr1:172939600-172945000	Weak transcription	Hela-S3	cervix
22	chr1:172939800-172945400	Weak transcription	NHLF	lung
23	chr1:172940000-172942400	Weak transcription	Osteobl	bone
24	chr1:172940000-172944800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:172940200-172941400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:172940400-172940800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:172940400-172940800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:172940400-172940800	Enhancers	Esophagus	oesophagus
29	chr1:172940400-172940800	Enhancers	Gastric	stomach
30	chr1:172940400-172941600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:172940400-172941800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:172940400-172943200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:172940600-172941200	Weak transcription	HSMM	muscle
34	chr1:172940600-172941400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:172940600-172941800	Enhancers	Fetal Lung	lung
36	chr1:172940600-172944800	Weak transcription	HUVEC	blood vessel
37	chr1:172940600-172945200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links