Variant report

Variant	rs638763
Chromosome Location	chr18:39564161-39564162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1787173	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1788988	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1944967	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4447506	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs477256	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs484350	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs500086	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs503472	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs511605	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs514227	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs515626	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517864	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519465	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs523425	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524793	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525399	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs52911	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530113	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs531258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs533028	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs535626	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs555734	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559231	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs573835	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs577955	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs587686	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs590912	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593248	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600658	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609301	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620052	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs620344	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622612	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs622939	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs625896	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627636	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs629481	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs639656	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs647512	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs649610	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664338	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693020	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers 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	4 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs638763	PIK3C3	cis	parietal	SCAN
rs638763	PIK3C3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
2	chr18:39536200-39564800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:39536200-39568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:39536400-39578200	Weak transcription	A549	lung
5	chr18:39536800-39580000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr18:39545600-39583600	Weak transcription	Small Intestine	intestine
8	chr18:39547400-39564600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr18:39547600-39580600	Weak transcription	Spleen	Spleen
10	chr18:39547800-39569000	Weak transcription	Fetal Brain Female	brain
11	chr18:39548000-39576000	Weak transcription	Fetal Brain Male	brain
12	chr18:39548000-39580200	Weak transcription	Pancreas	Pancrea
13	chr18:39548200-39564600	Weak transcription	Esophagus	oesophagus
14	chr18:39548200-39564800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr18:39548200-39569200	Weak transcription	Ovary	ovary
16	chr18:39548200-39576600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr18:39548200-39579400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr18:39548200-39580200	Weak transcription	Lung	lung
19	chr18:39548200-39580400	Weak transcription	NHLF	lung
20	chr18:39548400-39573400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:39548400-39576000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr18:39548600-39573400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr18:39548800-39564800	Weak transcription	HepG2	liver
25	chr18:39549000-39576800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr18:39549200-39582800	Weak transcription	Psoas Muscle	Psoas
27	chr18:39550400-39577000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr18:39551000-39564600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr18:39551000-39567600	Weak transcription	Fetal Lung	lung
30	chr18:39551000-39573400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr18:39551000-39576200	Weak transcription	Left Ventricle	heart
32	chr18:39551200-39564600	Weak transcription	Osteobl	bone
33	chr18:39551400-39564600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr18:39551400-39569000	Weak transcription	Brain Germinal Matrix	brain
35	chr18:39551400-39573400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr18:39551400-39576600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr18:39551600-39564400	Weak transcription	Adipose Nuclei	Adipose
38	chr18:39551600-39568200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr18:39551800-39564600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr18:39552000-39564600	Weak transcription	Placenta	Placenta
41	chr18:39552400-39568000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr18:39552600-39564600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr18:39552600-39570000	Weak transcription	NHDF-Ad	bronchial
44	chr18:39552800-39564600	Weak transcription	NH-A	brain
45	chr18:39552800-39567800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr18:39552800-39580200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr18:39553000-39564400	Weak transcription	Thymus	Thymus
48	chr18:39553000-39564600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr18:39553000-39569000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr18:39554200-39574000	Weak transcription	Colon Smooth Muscle	Colon

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