Variant report

Variant	rs11120540
Chromosome Location	chr1:215456074-215456075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10494997	0.91[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	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120531	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11811604	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12026152	0.91[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	0.82[AFR][1000 genomes];0.93[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];0.89[EUR][1000 genomes]
rs1339399	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339400	0.97[ASN][1000 genomes]
rs1361342	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1416651	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416653	0.80[AFR][1000 genomes]
rs1416656	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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];0.87[EUR][1000 genomes]
rs4633261	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4655280	0.98[AFR][1000 genomes];0.93[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	0.91[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]
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
rs11120540	LQK1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215451600-215458200	Weak transcription	Fetal Lung	lung
2	chr1:215451600-215458400	Weak transcription	NHDF-Ad	bronchial
3	chr1:215454400-215456600	Enhancers	HUVEC	blood vessel
4	chr1:215454800-215456200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:215455600-215456200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:215455600-215456400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:215455800-215456200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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