Variant report

Variant	rs1431477
Chromosome Location	chr9:103954453-103954454
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103948158..103950502-chr9:103953516..103956648,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10113988	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10117175	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10121939	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10156478	0.90[MEX][hapmap]
rs10989422	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10989423	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10989424	0.83[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10989425	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10989426	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12336617	0.83[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12336728	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12338716	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12339921	0.83[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12339994	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12342841	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12344631	0.90[MEX][hapmap];0.83[AMR][1000 genomes]
rs12345075	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12345440	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12346158	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12346223	0.91[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12346256	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12347855	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12349128	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12350583	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12351067	0.83[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12352151	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12353249	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12685239	0.83[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12686592	0.83[CEU][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16920038	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16920055	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2116285	0.83[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2987734	0.91[JPT][hapmap]
rs57056311	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58661374	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61342570	0.82[AMR][1000 genomes]
rs61654883	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67133619	0.83[AMR][1000 genomes]
rs7029916	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs735847	0.83[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831671	chr9:103858107-104020816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv948791	chr9:103893030-103964650	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1431477	STX17	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103953200-103963600	Weak transcription	HepG2	liver
2	chr9:103954000-103954800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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