Variant report

Variant	rs12171276
Chromosome Location	chr3:179594590-179594591
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1073072	0.82[LWK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs12487519	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs12488582	0.99[EUR][1000 genomes]
rs13083814	0.91[EUR][1000 genomes]
rs13085715	0.99[EUR][1000 genomes]
rs13091962	0.93[EUR][1000 genomes]
rs13097749	0.89[EUR][1000 genomes]
rs1404272	0.80[CEU][hapmap]
rs17691629	0.93[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs17691869	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17692126	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs28651290	0.97[EUR][1000 genomes]
rs34446871	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs34849178	0.94[EUR][1000 genomes]
rs62291649	0.93[EUR][1000 genomes]
rs67980618	0.97[EUR][1000 genomes]
rs9822592	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9842990	0.80[YRI][hapmap]
rs9843845	0.86[AFR][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
rs12171276	PIK3CA	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179533800-179605000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:179537800-179599400	Weak transcription	Brain Anterior Caudate	brain
3	chr3:179564200-179606000	Strong transcription	Dnd41	blood
4	chr3:179571400-179596800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:179580200-179598600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:179590600-179598800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:179591000-179600400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:179591600-179596800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:179593800-179596800	Weak transcription	Brain Hippocampus Middle	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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