Variant report

Variant	rs1057390
Chromosome Location	chr2:209358951-209358952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:209356910..209360822-chr2:209361905..209365197,3	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10172914	0.86[CHB][hapmap]
rs10175739	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10182087	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10182685	0.80[ASN][1000 genomes]
rs10186531	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10193961	0.84[EUR][1000 genomes]
rs10208191	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10208295	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10210393	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10497902	0.86[CHB][hapmap]
rs10932256	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10932259	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11897897	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899172	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1259699	0.82[CEU][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1259700	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs12617780	0.96[ASN][1000 genomes]
rs12623816	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12694109	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13391882	0.90[ASN][1000 genomes]
rs13415155	0.83[ASN][1000 genomes]
rs1370375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1370377	1.00[JPT][hapmap]
rs1437414	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1595329	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs16840864	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16841092	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16841231	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16841233	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16841234	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs16841242	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs16841294	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1866044	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1866045	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1869534	0.90[ASN][1000 genomes]
rs1869535	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1898435	0.90[ASN][1000 genomes]
rs1898436	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2363468	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3856350	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4234089	0.85[CEU][hapmap]
rs4462735	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs4558530	0.93[ASN][1000 genomes]
rs4673395	1.00[JPT][hapmap]
rs4675748	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4675750	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4675751	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs56875378	0.83[ASN][1000 genomes]
rs57164492	0.83[ASN][1000 genomes]
rs58644588	0.83[ASN][1000 genomes]
rs60916150	0.93[ASN][1000 genomes]
rs61195726	0.93[ASN][1000 genomes]
rs6713477	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6716615	0.82[CEU][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6717082	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6721780	1.00[JPT][hapmap]
rs6725548	0.90[ASN][1000 genomes]
rs6725932	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6742461	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6752329	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7570304	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7583022	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs7595880	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7605626	0.80[ASN][1000 genomes]
rs9288394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs959660	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs962595	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9646839	0.88[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1057390	PIKFYVE	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209355200-209361000	Weak transcription	Stomach Mucosa	stomach
2	chr2:209355200-209366000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:209356600-209361000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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