Variant report

Variant	rs6788525
Chromosome Location	chr3:177720393-177720394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16828884	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1895070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080668	1.00[ASN][1000 genomes]
rs2863063	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4502028	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4533667	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579029	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56965193	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57660332	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283969	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283971	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283973	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283974	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283978	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283981	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763564	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764673	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767647	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804858	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727335	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7430015	1.00[ASN][1000 genomes]
rs7645340	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290631	1.00[ASN][1000 genomes]
rs9290633	1.00[ASN][1000 genomes]
rs9757291	1.00[ASN][1000 genomes]
rs9852369	1.00[ASN][1000 genomes]
rs9861535	1.00[ASN][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	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv829805	chr3:177662113-177805003	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6788525	PIK3CA	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177717800-177722600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:177718400-177725000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:177718600-177720600	Enhancers	Primary B cells from cord blood	blood
4	chr3:177718600-177720600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:177718600-177722400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:177718600-177722600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:177719000-177721200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr3:177719000-177722200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:177719200-177720400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr3:177719200-177720600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:177719200-177722000	Enhancers	Dnd41	blood
12	chr3:177719400-177720400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:177719400-177720400	Enhancers	Thymus	Thymus
14	chr3:177719400-177720600	Enhancers	Fetal Thymus	thymus
15	chr3:177719600-177720400	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:177720000-177720400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr3:177720000-177720800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:177720000-177721000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:177720000-177721200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:177720000-177722400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:177720000-177722800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr3:177720000-177724800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr3:177720000-177725200	Enhancers	Primary T cells from cord blood	blood
24	chr3:177720200-177722400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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