Variant report

Variant	rs17670396
Chromosome Location	chr16:10059322-10059323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10518151	0.87[ASW][hapmap];1.00[MEX][hapmap]
rs1070479	0.85[CEU][hapmap]
rs1111537	0.81[CEU][hapmap]
rs11866570	1.00[MEX][hapmap]
rs13331514	1.00[MEX][hapmap]
rs13336632	0.82[MEX][hapmap]
rs1375075	1.00[CEU][hapmap]
rs1448262	1.00[MEX][hapmap]
rs1448268	0.81[CEU][hapmap]
rs1448272	0.81[CEU][hapmap]
rs17569609	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes]
rs17569693	0.87[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs17569940	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs17670318	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17670509	0.94[EUR][1000 genomes]
rs17670766	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs17671033	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs1827197	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2197778	0.82[MEX][hapmap]
rs2315510	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs3897996	0.97[EUR][1000 genomes]
rs4107019	0.81[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4254328	0.96[EUR][1000 genomes]
rs4780784	0.81[CEU][hapmap]
rs4998386	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes]
rs57497843	1.00[EUR][1000 genomes]
rs57576479	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59775432	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60547225	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7188291	1.00[MEX][hapmap]
rs7190619	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs7190716	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes]
rs7191736	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7192121	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7193123	0.86[EUR][1000 genomes]
rs7193471	0.82[EUR][1000 genomes]
rs7197048	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7197200	1.00[MEX][hapmap]
rs7200719	0.81[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7201627	0.81[CEU][hapmap]
rs7203194	1.00[MEX][hapmap]
rs72772131	0.97[EUR][1000 genomes]
rs72772153	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72772155	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72772157	0.99[EUR][1000 genomes]
rs72772164	0.97[EUR][1000 genomes]
rs72772166	0.96[EUR][1000 genomes]
rs72772167	0.94[EUR][1000 genomes]
rs72772168	0.93[EUR][1000 genomes]
rs72772169	0.93[EUR][1000 genomes]
rs72772342	0.82[EUR][1000 genomes]
rs72772347	0.86[EUR][1000 genomes]
rs72772360	0.82[EUR][1000 genomes]
rs72772361	0.82[EUR][1000 genomes]
rs72772364	0.82[EUR][1000 genomes]
rs72774046	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72774047	0.86[EUR][1000 genomes]
rs72774048	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72774051	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72774055	0.86[EUR][1000 genomes]
rs72774059	0.85[EUR][1000 genomes]
rs72774081	0.86[EUR][1000 genomes]
rs8043728	0.81[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8045558	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8058978	1.00[GIH][hapmap]
rs9302409	1.00[MEX][hapmap]
rs9922383	1.00[MEX][hapmap]
rs9922871	0.87[ASW][hapmap];1.00[MEX][hapmap]
rs9925439	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9929020	0.93[EUR][1000 genomes]
rs9930364	1.00[MEX][hapmap]
rs9933111	1.00[MEX][hapmap]
rs9935774	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949196	chr16:9937980-10182349	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1037001	chr16:10008023-10476482	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422500	chr16:10008309-10415517	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1045882	chr16:10025402-10117992	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1052566	chr16:10033178-10260068	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv905333	chr16:10055461-10079124	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17670396	CA2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:10049000-10063000	Weak transcription	Brain Angular Gyrus	brain
2	chr16:10051000-10059400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr16:10058000-10063800	Weak transcription	Aorta	Aorta
4	chr16:10058800-10059400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr16:10059000-10059400	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr16:10059000-10059600	Enhancers	Brain Anterior Caudate	brain
7	chr16:10059000-10059600	Enhancers	Brain Cingulate Gyrus	brain

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