Talk:Rs1558902

Is this SNP in LD with rs9939609?

Cheers

On 1kG CEU:

SNP	Proxy	Distance	RSquared	DPrime	Chromosome	Coordinate_HG18	RecombinationRate	GeneticMapDistance	Major	Minor	MAF	NObserved
rs1558902	rs1421085	2620	1.000	1.000	chr16	52358455	0.03340	0.00077	T	C	0.458	120
rs1558902	rs17817449	9793	0.901	0.965	chr16	52370868	0.08897	0.00374	T	G	0.450	120
rs1558902	rs9939609	16953	0.901	0.965	chr16	52378028	0.01049	0.00522	T	A	0.450	120
rs9939609	rs17817449	7160	1.000	1.000	chr16	52370868	0.08897	0.00148	T	G	0.450	120
rs9939609	rs1558902	16953	0.901	0.965	chr16	52361075	0.20590	0.00522	T	A	0.458	120
rs9939609	rs1421085	19573	0.901	0.965	chr16	52358455	0.03340	0.00598	T	C	0.458	120
rs17817449	rs9939609	7160	1.000	1.000	chr16	52378028	0.01049	0.00148	T	A	0.450	120
rs17817449	rs1558902	9793	0.901	0.965	chr16	52361075	0.20590	0.00374	T	A	0.458	120
rs17817449	rs1421085	12413	0.901	0.965	chr16	52358455	0.03340	0.00450	T	C	0.458	120
rs1421085	rs1558902	2620	1.000	1.000	chr16	52361075	0.20590	0.00077	T	A	0.458	120
rs1421085	rs17817449	12413	0.901	0.965	chr16	52370868	0.08897	0.00450	T	G	0.450	120
rs1421085	rs9939609	19573	0.901	0.965	chr16	52378028	0.01049	0.00598	T	A	0.450	120

Via http://www.broadinstitute.org/mpg/snap/ldsearchpw.php

However, on other population panels the results get little wonky. They have D' 1.0 for all, but R^2 for the pair you're asking is down to 0.06 for YRI. This is because A-allele frequency of rs1558902 is only 0.07 there, so while the SNP's are inherited together they don't predict each other on non straight CEU populations. --Donwulff (talk) 23:09, 27 May 2014 (UTC)