Variant report

Variant	rs2160354
Chromosome Location	chr14:80742107-80742108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10131076	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10133463	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10140980	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10144099	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10146631	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149251	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10150064	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10150190	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10483947	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11159454	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11851891	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1388378	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17110449	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17110492	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17110521	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1884071	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1907526	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1955625	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2160355	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267872	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2267873	0.81[TSI][hapmap]
rs2273173	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2295138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607034	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28883971	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55859799	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55884286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56033314	0.89[EUR][1000 genomes]
rs61989398	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6574551	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7140952	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7141617	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7145153	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7145584	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7146189	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7154177	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7154898	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7159642	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7159995	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7160310	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs73335280	0.82[AFR][1000 genomes]
rs7350729	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8003183	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8009555	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8011716	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9652301	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9972105	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9972275	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[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	nsv902113	chr14:80172094-80929699	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv902115	chr14:80700351-80844239	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1371	chr14:80719478-80761504	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2160354	NRXN3	cis	parietal	SCAN
rs2160354	KIAA1737	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:80735400-80744800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:80737200-80744800	Weak transcription	Esophagus	oesophagus
3	chr14:80741000-80742200	Enhancers	HSMMtube	muscle
4	chr14:80741000-80744000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:80741200-80744800	Weak transcription	Psoas Muscle	Psoas
6	chr14:80741400-80742200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr14:80741400-80742200	Enhancers	NH-A	brain
8	chr14:80741600-80742200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:80741800-80742600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr14:80741800-80744600	Weak transcription	NHLF	lung

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