Variant report

Variant	rs8087875
Chromosome Location	chr18:39630347-39630348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10502776	0.92[ASW][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11082256	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12605021	0.83[ASN][1000 genomes]
rs12606434	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12607810	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12953847	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12954899	0.91[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs12956553	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12957030	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12959405	0.82[EUR][1000 genomes]
rs12961563	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12962602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12962732	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1544260	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960213	0.84[ASN][1000 genomes]
rs16975459	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975462	0.82[ASN][1000 genomes]
rs28438873	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28541909	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28566843	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28708684	0.84[ASN][1000 genomes]
rs35269653	0.87[EUR][1000 genomes]
rs3813065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3819162	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4121817	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4283305	0.82[EUR][1000 genomes]
rs4513183	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55971157	0.85[ASN][1000 genomes]
rs56680148	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61682064	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62082284	0.80[EUR][1000 genomes]
rs62082292	0.87[EUR][1000 genomes]
rs62082876	0.84[EUR][1000 genomes]
rs7230624	0.92[ASN][1000 genomes]
rs7230883	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7233661	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7237737	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237780	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237783	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7238178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7239652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7240218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241401	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7242727	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73454598	0.82[ASN][1000 genomes]
rs8092954	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8095411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646518	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs9949409	0.83[ASN][1000 genomes]
rs9949895	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9954624	0.82[ASN][1000 genomes]
rs9956832	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9958749	0.83[ASN][1000 genomes]
rs9964331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9965466	0.82[ASN][1000 genomes]
rs9966146	0.84[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	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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8087875	PIK3C3	cis	parietal	SCAN
rs8087875	PIK3C3	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
4	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
5	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
6	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:39585000-39646000	Weak transcription	Pancreas	Pancrea
8	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
9	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
10	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
11	chr18:39594600-39638800	Weak transcription	K562	blood
12	chr18:39599000-39646000	Weak transcription	Psoas Muscle	Psoas
13	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr18:39607600-39634600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr18:39608800-39631400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr18:39609200-39631400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr18:39609200-39631600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr18:39609800-39630400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:39612200-39647400	Weak transcription	Aorta	Aorta
20	chr18:39612200-39666400	Weak transcription	Gastric	stomach
21	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
22	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr18:39613800-39631200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr18:39613800-39631400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr18:39614400-39631400	Strong transcription	Primary B cells from cord blood	blood
26	chr18:39615000-39649600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr18:39615400-39663400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr18:39618000-39647400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr18:39619200-39656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr18:39619400-39633400	Weak transcription	Brain Substantia Nigra	brain
31	chr18:39619400-39647600	Weak transcription	Brain Germinal Matrix	brain
32	chr18:39619600-39632400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr18:39619600-39645600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr18:39619600-39647400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr18:39619800-39662200	Weak transcription	Right Ventricle	heart
36	chr18:39620200-39645800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr18:39620800-39664200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr18:39621200-39646200	Weak transcription	Lung	lung
39	chr18:39621200-39657200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr18:39621600-39644800	Weak transcription	Ovary	ovary
41	chr18:39621800-39644800	Weak transcription	Placenta	Placenta
42	chr18:39622000-39630400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr18:39622200-39638400	Weak transcription	HSMMtube	muscle
44	chr18:39622200-39649400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr18:39622400-39632800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr18:39622400-39634600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr18:39623000-39633000	Weak transcription	Brain Angular Gyrus	brain
48	chr18:39625200-39631800	Strong transcription	GM12878-XiMat	blood
49	chr18:39625400-39631000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr18:39626000-39630400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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