Variant report

Variant	rs627636
Chromosome Location	chr18:39678828-39678829
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11659568	0.90[EUR][1000 genomes]
rs11660388	0.90[EUR][1000 genomes]
rs11660513	0.90[EUR][1000 genomes]
rs12327365	0.89[EUR][1000 genomes]
rs12709716	0.85[EUR][1000 genomes]
rs12954202	0.86[EUR][1000 genomes]
rs1557419	0.89[EUR][1000 genomes]
rs1787173	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1788988	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1944967	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2096896	0.89[EUR][1000 genomes]
rs2096897	0.89[EUR][1000 genomes]
rs2105680	0.89[EUR][1000 genomes]
rs3932738	0.89[EUR][1000 genomes]
rs3932739	0.89[EUR][1000 genomes]
rs4121811	0.87[EUR][1000 genomes]
rs4447506	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs477256	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs484350	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500086	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs503472	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs514227	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515626	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs517864	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs519465	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs523425	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs524793	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs525399	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs52911	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs530113	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531258	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs533028	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs535626	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536139	0.90[EUR][1000 genomes]
rs555734	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs559231	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs573835	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs577955	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs582268	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs584380	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs587686	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs590912	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs593248	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs600658	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs609301	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs620052	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs620344	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs622612	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs622939	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs625896	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs629481	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs638763	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs639656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs647512	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs649610	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs664338	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs681048	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs693020	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7237998	0.83[EUR][1000 genomes]
rs948871	0.86[EUR][1000 genomes]
rs948872	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1057988	chr18:39618253-39713904	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1065792	chr18:39619676-39711798	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv1057790	chr18:39621947-39705550	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	esv2762006	chr18:39621947-39713916	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv1063952	chr18:39621947-39718600	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1064973	chr18:39623604-39711798	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv833631	chr18:39633503-39824091	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1063205	chr18:39678456-39741061	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv1060346	chr18:39678456-39742702	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs627636	PIK3C3	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39653000-39683400	Weak transcription	Aorta	Aorta
2	chr18:39676800-39680200	Weak transcription	Fetal Intestine Large	intestine

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