Variant report

Variant	rs1416656
Chromosome Location	chr1:215466086-215466087
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	chr1:215460715..215462966-chr1:215464871..215466869,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10494997	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10779655	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10864162	0.86[EUR][1000 genomes]
rs10864163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10864164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11120522	0.88[EUR][1000 genomes]
rs11120528	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120531	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120540	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811604	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12026152	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12080135	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs12131712	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12142076	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1339399	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339400	0.97[ASN][1000 genomes]
rs1361342	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1416651	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416653	0.83[AFR][1000 genomes]
rs2202679	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4281301	0.97[EUR][1000 genomes]
rs4360503	0.88[EUR][1000 genomes]
rs4375236	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4539107	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4633261	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4655280	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664253	0.80[EUR][1000 genomes]
rs6671986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6674923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6704340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72737267	0.97[ASN][1000 genomes]
rs7512197	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7531046	0.83[AFR][1000 genomes]
rs7547867	0.88[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	nsv1014878	chr1:215453286-215527616	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1003660	chr1:215453286-215529747	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1416656	LQK1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215466000-215466200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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