Variant report

Variant	rs3118059
Chromosome Location	chr1:58235497-58235498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1155492	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323816	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs1323820	0.81[ASN][1000 genomes]
rs1323821	0.85[CHD][hapmap]
rs1323824	0.82[CHD][hapmap]
rs1323825	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs1323827	0.91[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1886140	0.93[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1924265	0.81[ASN][1000 genomes]
rs2406282	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3118050	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3118053	0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3118054	0.88[ASN][1000 genomes]
rs3118055	0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3118057	0.91[ASN][1000 genomes]
rs3118058	0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3118063	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs3131735	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131736	0.83[ASN][1000 genomes]
rs3131737	0.83[ASN][1000 genomes]
rs3131738	0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3131740	0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3131741	0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3131742	0.91[ASN][1000 genomes]
rs3131743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131745	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs723572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs927612	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs978786	0.85[ASN][1000 genomes]

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	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3118059	YIPF1	cis	cerebellum	SCAN
rs3118059	NFIA	cis	cerebellum	SCAN
rs3118059	PARS2	cis	parietal	SCAN
rs3118059	NID1	trans	lymphoblastoid	seeQTL
rs3118059	GADL1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58233000-58238600	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links