Variant report

Variant	rs4916290
Chromosome Location	chr1:172914284-172914285
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172908894..172911352-chr1:172913551..172915186,2	MCF-7	breast:
2	chr1:172909766..172912196-chr1:172914192..172916042,2	K562	blood:
3	chr1:172913673..172916975-chr1:172918949..172922757,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489274	0.82[EUR][1000 genomes]
rs10798243	0.82[EUR][1000 genomes]
rs10798244	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10912491	0.80[ASN][1000 genomes]
rs10912499	0.83[EUR][1000 genomes]
rs10912501	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10912502	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12025176	0.80[ASN][1000 genomes]
rs12402215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12409216	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12410129	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12565596	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12567579	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12748081	0.80[ASN][1000 genomes]
rs1883475	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051629	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2179425	0.82[EUR][1000 genomes]
rs2187893	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2206363	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2206364	0.81[EUR][1000 genomes]
rs2206365	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2206366	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35715673	0.80[ASN][1000 genomes]
rs4145468	0.80[ASN][1000 genomes]
rs4145469	0.86[CEU][hapmap];0.91[MEX][hapmap]
rs4916287	0.85[EUR][1000 genomes]
rs4916288	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4916289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668693	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6674470	0.83[EUR][1000 genomes]
rs6688532	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs7517726	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7539951	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs926472	0.81[EUR][1000 genomes]
rs9283384	0.82[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4916290	C1orf114	cis	parietal	SCAN
rs4916290	SNORD47	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172905600-172916000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:172910800-172916200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:172911000-172914400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:172911200-172914400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:172911200-172915800	Weak transcription	NHDF-Ad	bronchial
6	chr1:172911200-172916000	Weak transcription	HSMMtube	muscle
7	chr1:172911200-172916200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:172911200-172917000	Weak transcription	Fetal Stomach	stomach
9	chr1:172911200-172917600	Weak transcription	Fetal Lung	lung
10	chr1:172911400-172916000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:172911400-172916000	Weak transcription	NH-A	brain
12	chr1:172913600-172919200	Enhancers	HUVEC	blood vessel
13	chr1:172914200-172914400	Enhancers	Aorta	Aorta
14	chr1:172914200-172914800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:172914200-172915000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links