Variant report

Variant	rs2420109
Chromosome Location	chr10:117487861-117487862
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	chr10:117479183..117481375-chr10:117486927..117488986,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10490919	0.85[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10885772	1.00[JPT][hapmap]
rs10885789	1.00[JPT][hapmap]
rs10885796	0.83[AMR][1000 genomes]
rs10885797	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10885799	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10885801	0.84[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885810	0.81[CEU][hapmap]
rs11197429	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1157117	0.84[CEU][hapmap]
rs12219077	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12777802	0.86[JPT][hapmap]
rs12784311	0.86[JPT][hapmap]
rs1547948	0.80[JPT][hapmap]
rs2243740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286631	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2420110	0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2420111	0.85[CEU][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs2420116	0.80[JPT][hapmap]
rs2532709	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2804160	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2804161	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2960715	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4600124	0.85[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4751930	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6585362	0.80[JPT][hapmap]
rs7923360	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs961155	0.80[JPT][hapmap]
rs991389	0.84[CHB][hapmap]
rs992888	1.00[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2420109	TECTB	cis	parietal	SCAN
rs2420109	GFRA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:117471000-117490600	Weak transcription	Aorta	Aorta

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