Variant report

Variant	rs17418048
Chromosome Location	chr1:56100997-56100998
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	chr1:56100834..56102413-chr1:56105064..56106750,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1039294	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10493193	0.85[CEU][hapmap]
rs10493194	0.85[CEU][hapmap]
rs10493195	0.85[CEU][hapmap]
rs11206626	0.85[CEU][hapmap]
rs11206635	0.92[CEU][hapmap]
rs11206649	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11801001	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11805740	0.92[CEU][hapmap]
rs12116670	0.85[CEU][hapmap]
rs12117758	0.85[CEU][hapmap]
rs12124658	0.87[EUR][1000 genomes]
rs12125730	0.90[CEU][hapmap]
rs12139482	0.85[CEU][hapmap]
rs17418151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17418627	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17452287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4412634	1.00[JPT][hapmap]
rs4575120	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58623222	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6588567	0.85[CEU][hapmap]
rs6670673	0.85[CEU][hapmap]
rs6680818	0.85[CEU][hapmap]
rs6681925	0.85[CEU][hapmap]
rs6694786	0.92[CEU][hapmap]
rs7519540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548272	0.85[CEU][hapmap]
rs7549716	0.85[CEU][hapmap]
rs7550575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs769989	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17418048	ZYG11A	cis	parietal	SCAN
rs17418048	GLIS1	cis	cerebellum	SCAN
rs17418048	ACOT11	cis	parietal	SCAN
rs17418048	CPT2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56089000-56104000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:56096000-56103400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:56096800-56102800	Enhancers	Osteobl	bone
4	chr1:56097000-56103000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:56097000-56103400	Enhancers	NHDF-Ad	bronchial
6	chr1:56098000-56101200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:56098000-56101800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:56098400-56102200	Enhancers	NHLF	lung
9	chr1:56098800-56105800	Weak transcription	Fetal Stomach	stomach
10	chr1:56099000-56105200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:56099000-56106600	Weak transcription	Ovary	ovary
12	chr1:56099200-56105800	Weak transcription	Fetal Kidney	kidney
13	chr1:56099400-56101600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:56099600-56101800	Enhancers	Aorta	Aorta
15	chr1:56100000-56101200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:56100000-56102600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:56100200-56101200	Enhancers	Psoas Muscle	Psoas
18	chr1:56100400-56101000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:56100600-56101200	Enhancers	Esophagus	oesophagus
20	chr1:56100600-56101600	Weak transcription	Fetal Lung	lung
21	chr1:56100600-56102400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:56100600-56106600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:56100800-56102400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:56100800-56104800	Weak transcription	Hela-S3	cervix
25	chr1:56100800-56106600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links