Variant report

Variant	rs11927258
Chromosome Location	chr3:102097328-102097329
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10511197	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs10511198	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1108689	0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs11720144	0.82[TSI][hapmap]
rs12233481	0.82[TSI][hapmap]
rs13317906	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1369350	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1382787	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1382788	0.80[CEU][hapmap]
rs1435206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1585772	0.80[CEU][hapmap]
rs1585774	0.80[CEU][hapmap]
rs1600328	0.80[CEU][hapmap]
rs1600329	0.80[CEU][hapmap]
rs16844993	0.88[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs17822656	0.88[JPT][hapmap]
rs1993928	0.80[CEU][hapmap]
rs2164264	0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs55654405	0.85[ASN][1000 genomes]
rs55891453	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56057951	0.85[ASN][1000 genomes]
rs56132352	0.81[ASN][1000 genomes]
rs56224182	0.81[ASN][1000 genomes]
rs62274710	0.81[ASN][1000 genomes]
rs62274711	0.83[ASN][1000 genomes]
rs6441655	0.80[CEU][hapmap]
rs6766223	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs6779934	0.80[CEU][hapmap]
rs6804554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73157654	0.81[ASN][1000 genomes]
rs7615419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7635093	0.80[CEU][hapmap]
rs7637090	0.80[CEU][hapmap]
rs7644557	0.80[CEU][hapmap]
rs9838540	0.80[CEU][hapmap]
rs985376	0.92[ASN][1000 genomes]
rs9875116	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877227	chr3:102067254-102184308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv460790	chr3:102089007-102100781	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
3	nsv460791	chr3:102089007-102100781	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
4	nsv591189	chr3:102089007-102100781	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11927258	PIF1	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:102096400-102098000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:102096600-102097600	Enhancers	HMEC	breast
3	chr3:102096600-102098000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:102097200-102097600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:102097200-102097600	Flanking Active TSS	NHEK	skin

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