Variant report

Variant	rs774139
Chromosome Location	chr1:220908088-220908089
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220905806..220908552-chr1:220910412..220912750,2	K562	blood:
2	chr1:220905522..220909256-chr1:220918149..220921942,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11589296	0.87[EUR][1000 genomes]
rs12032280	0.85[EUR][1000 genomes]
rs12407624	1.00[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs12563921	0.81[EUR][1000 genomes]
rs12564479	0.83[EUR][1000 genomes]
rs1472253	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1494373	0.89[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs17008587	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2275575	0.89[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs337156	0.83[AMR][1000 genomes]
rs337157	0.83[TSI][hapmap]
rs337159	0.83[AMR][1000 genomes]
rs337162	0.83[AMR][1000 genomes]
rs337163	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337165	0.83[AMR][1000 genomes]
rs337166	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs337167	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337168	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs337174	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs337182	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337188	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs337192	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3753879	0.89[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs3806329	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs41314538	0.87[EUR][1000 genomes]
rs4846658	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59423796	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61830238	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs774139	C1orf115	cis	multi-tissue	Pritchard
rs774139	C1orf115	cis	cerebellum	SCAN
rs774139	EPRS	cis	cerebellum	SCAN
rs774139	TGFB2	cis	cerebellum	SCAN
rs774139	MOSC2	cis	cerebellum	SCAN
rs774139	MOSC1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220905600-220908600	Enhancers	NHLF	lung
2	chr1:220905800-220908600	Enhancers	Placenta	Placenta
3	chr1:220906000-220908400	Enhancers	HMEC	breast
4	chr1:220906000-220908400	Enhancers	NHEK	skin
5	chr1:220906000-220908600	Enhancers	Fetal Intestine Large	intestine
6	chr1:220906000-220908600	Enhancers	NHDF-Ad	bronchial
7	chr1:220906200-220908400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:220906200-220908600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:220906400-220908200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:220906400-220908600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:220906400-220908600	Enhancers	Fetal Intestine Small	intestine
12	chr1:220906400-220921000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:220906600-220908600	Enhancers	Stomach Mucosa	stomach
14	chr1:220906800-220908200	Enhancers	Duodenum Mucosa	Duodenum
15	chr1:220906800-220908600	Flanking Active TSS	A549	lung
16	chr1:220907000-220908400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:220907000-220908400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:220907000-220908400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:220907000-220908400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:220907000-220908400	Enhancers	NH-A	brain
21	chr1:220907000-220908600	Enhancers	Osteobl	bone
22	chr1:220907200-220908200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr1:220907200-220908400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:220907200-220908400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:220907200-220908600	Enhancers	HUVEC	blood vessel
26	chr1:220907400-220908200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:220907400-220908400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:220907800-220908200	Active TSS	HepG2	liver
29	chr1:220907800-220908400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:220908000-220908200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr1:220908000-220908200	Enhancers	Ovary	ovary
32	chr1:220908000-220908400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:220908000-220908400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:220908000-220908400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:220908000-220908400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:220908000-220908400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:220908000-220908400	Flanking Active TSS	Aorta	Aorta
38	chr1:220908000-220908400	Enhancers	Pancreas	Pancrea
39	chr1:220908000-220908400	Enhancers	Rectal Smooth Muscle	rectum
40	chr1:220908000-220908400	Enhancers	Small Intestine	intestine
41	chr1:220908000-220908400	Flanking Active TSS	Hela-S3	cervix
42	chr1:220908000-220908400	Enhancers	HSMM	muscle
43	chr1:220908000-220908400	Enhancers	HSMMtube	muscle
44	chr1:220908000-220908600	Flanking Active TSS	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links