Variant report

Variant	rs17691629
Chromosome Location	chr3:179614511-179614512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12171276	0.93[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs12487519	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12488582	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13083814	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13085715	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13091962	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13097749	0.90[EUR][1000 genomes]
rs1404272	0.87[CEU][hapmap];0.86[AFR][1000 genomes]
rs17691869	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17692126	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[GIH][hapmap];0.92[MKK][hapmap];0.86[AFR][1000 genomes]
rs28651290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34446871	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34849178	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62291649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67980618	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9822592	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.97[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	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17691629	PIK3CA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179601200-179624200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:179606000-179626600	Weak transcription	Dnd41	blood
3	chr3:179606200-179628800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:179610800-179622800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:179611000-179623400	Weak transcription	Brain Angular Gyrus	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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