Variant report

Variant	rs3932739
Chromosome Location	chr18:39686612-39686613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10221315	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10468957	0.93[ASN][1000 genomes]
rs11082255	0.83[CHB][hapmap]
rs11659568	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11660388	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11660513	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11662171	0.86[EUR][1000 genomes]
rs12326267	0.93[ASN][1000 genomes]
rs12327365	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12455083	0.83[CHB][hapmap]
rs12457082	0.84[ASN][1000 genomes]
rs12457086	0.84[ASN][1000 genomes]
rs12709716	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12954202	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12964931	0.90[ASN][1000 genomes]
rs1557418	0.93[ASN][1000 genomes]
rs1557419	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573497	0.93[ASN][1000 genomes]
rs1787173	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs1788988	0.88[EUR][1000 genomes]
rs1941532	0.93[ASN][1000 genomes]
rs1944967	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs2096896	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096897	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105680	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3932738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121811	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4447506	0.84[CEU][hapmap]
rs477256	0.89[EUR][1000 genomes]
rs484350	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4890222	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4890377	0.86[CHB][hapmap]
rs4890379	0.83[CHB][hapmap]
rs500086	0.83[EUR][1000 genomes]
rs503472	0.89[EUR][1000 genomes]
rs511605	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs514227	0.87[EUR][1000 genomes]
rs515626	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs519465	0.90[EUR][1000 genomes]
rs525399	0.84[EUR][1000 genomes]
rs530113	0.83[EUR][1000 genomes]
rs531258	0.87[CEU][hapmap]
rs535626	0.90[EUR][1000 genomes]
rs536139	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55720287	0.80[AMR][1000 genomes]
rs56147258	0.93[ASN][1000 genomes]
rs577955	0.87[EUR][1000 genomes]
rs581950	0.87[CHB][hapmap]
rs582268	0.85[EUR][1000 genomes]
rs587686	0.85[EUR][1000 genomes]
rs593248	0.88[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs600658	0.87[EUR][1000 genomes]
rs620052	0.84[EUR][1000 genomes]
rs620344	0.84[EUR][1000 genomes]
rs62082911	0.91[ASN][1000 genomes]
rs622939	0.84[EUR][1000 genomes]
rs627636	0.89[EUR][1000 genomes]
rs639656	0.82[EUR][1000 genomes]
rs647512	0.84[EUR][1000 genomes]
rs657164	0.83[CHB][hapmap]
rs681048	0.81[EUR][1000 genomes]
rs693020	0.88[EUR][1000 genomes]
rs7237998	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs948871	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948872	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs948873	0.93[ASN][1000 genomes]
rs9635942	0.93[ASN][1000 genomes]
rs9807114	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3932739	PIK3C3	cis	cerebellum	SCAN
rs3932739	PIK3C3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39681200-39687800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:39684000-39689400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr18:39685200-39687200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:39685200-39689400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:39686400-39687400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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