Variant report

Variant	rs1552770
Chromosome Location	chr10:25360166-25360167
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	chr10:24854730..24857189-chr10:25359782..25362279,2	K562	blood:
2	chr10:25356543..25358700-chr10:25359934..25363281,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10508685	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10508686	0.87[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10828745	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10828747	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10828750	0.86[ASN][1000 genomes]
rs10828751	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10828752	0.93[ASN][1000 genomes]
rs10828754	0.96[ASN][1000 genomes]
rs10828755	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11014360	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11014361	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11014362	0.89[EUR][1000 genomes]
rs11014365	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs11014367	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11014368	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11014375	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014379	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014389	0.82[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1124017	0.81[EUR][1000 genomes]
rs12219239	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs12241661	0.85[EUR][1000 genomes]
rs12249889	0.93[GIH][hapmap]
rs12256642	0.93[GIH][hapmap]
rs12764623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12773782	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12776058	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12784769	0.80[CEU][hapmap]
rs1352984	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1352985	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1492606	0.82[CEU][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1492607	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492608	0.93[GIH][hapmap]
rs1546097	0.84[CEU][hapmap];0.95[GIH][hapmap]
rs1552771	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1907790	0.94[ASN][1000 genomes]
rs1907791	0.88[EUR][1000 genomes]
rs2087781	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2131275	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2220707	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2291583	0.93[GIH][hapmap]
rs2307047	0.93[GIH][hapmap]
rs4237369	0.94[EUR][1000 genomes]
rs4508094	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4747511	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4748996	0.93[GIH][hapmap]
rs4748999	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4749000	0.91[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs4749001	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4749004	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4749005	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6482468	0.82[CHB][hapmap]
rs7896122	0.94[EUR][1000 genomes]
rs7911863	0.94[EUR][1000 genomes]
rs902904	0.93[GIH][hapmap]
rs902906	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs923757	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs923758	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv550224	chr10:25335854-25385858	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1036683	chr10:25337592-25398119	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv894969	chr10:25345720-25395579	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1552770	PIP4K2A	cis	parietal	SCAN
rs1552770	ENKUR	cis	parietal	SCAN
rs1552770	THNSL1	cis	parietal	SCAN
rs1552770	THNSL1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25358000-25361400	Weak transcription	HUVEC	blood vessel
2	chr10:25360000-25360200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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