Variant report

Variant	rs4588684
Chromosome Location	chr6:25638067-25638068
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	chr6:25627142..25629729-chr6:25636254..25639061,2	K562	blood:
2	chr6:25629018..25631052-chr6:25636456..25638634,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1022492	0.80[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs12665641	0.88[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap]
rs13192159	0.87[CEU][hapmap]
rs13201652	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs13217586	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1406924	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16890880	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049967	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2072845	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072849	0.80[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs2205935	0.93[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2272824	0.84[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3747526	0.84[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3788992	0.84[AMR][1000 genomes]
rs3804120	0.87[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs3804124	0.80[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs3804126	0.80[CEU][hapmap]
rs3827505	0.80[CEU][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs57075629	0.81[AFR][1000 genomes]
rs6932016	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935799	0.80[CEU][hapmap]
rs6939153	0.93[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7738571	0.80[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs7739227	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7740510	0.94[GIH][hapmap]
rs7741329	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7767930	0.84[ASW][hapmap];0.87[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs7776417	0.80[CEU][hapmap]
rs9295665	0.87[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes]
rs9348683	0.80[CEU][hapmap]
rs9356983	0.85[AMR][1000 genomes]
rs9358865	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358866	0.86[EUR][1000 genomes]
rs9379772	0.80[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs9379776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379777	0.93[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs9393648	0.81[GIH][hapmap]
rs9393650	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs941428	0.89[EUR][1000 genomes];0.87[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	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4588684	GPX6	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25629000-25638200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25630200-25640800	Weak transcription	Pancreas	Pancrea
3	chr6:25632000-25638400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:25636600-25640600	Enhancers	HepG2	liver
5	chr6:25636600-25641800	Weak transcription	A549	lung
6	chr6:25637000-25642600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:25637200-25638600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:25637400-25638400	Weak transcription	Fetal Intestine Large	intestine
9	chr6:25637600-25639200	Enhancers	Brain Germinal Matrix	brain
10	chr6:25637800-25638600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:25638000-25638600	Enhancers	HUES48 Cell Line	embryonic stem cell

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