Variant report

Variant	rs12080135
Chromosome Location	chr1:215396543-215396544
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10494997	0.88[EUR][1000 genomes]
rs10779654	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779655	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10864162	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864163	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864164	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120528	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120531	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120540	0.88[EUR][1000 genomes]
rs11811604	0.84[EUR][1000 genomes]
rs12026152	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12131712	0.89[EUR][1000 genomes]
rs12142076	0.88[EUR][1000 genomes]
rs12567503	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339399	0.88[EUR][1000 genomes]
rs1361342	0.88[EUR][1000 genomes]
rs1416651	0.87[EUR][1000 genomes]
rs1416656	0.88[EUR][1000 genomes]
rs2202679	0.88[EUR][1000 genomes]
rs4113098	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281301	0.86[EUR][1000 genomes]
rs4360503	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375236	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4539107	0.93[CEU][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4633261	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4655280	0.86[EUR][1000 genomes]
rs6664253	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6671986	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674923	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704340	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7512197	0.88[EUR][1000 genomes]
rs7516344	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7547867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
2	nsv873170	chr1:215367248-215440975	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	nsv527715	chr1:215396543-215402022	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12080135	LQK1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215380600-215408000	Weak transcription	Osteobl	bone
2	chr1:215388600-215408200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:215389200-215401400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:215392000-215408000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:215394000-215407800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links