Variant report

Variant	rs584380
Chromosome Location	chr18:39693855-39693856
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11662171	0.91[EUR][1000 genomes]
rs12954202	0.80[EUR][1000 genomes]
rs1787173	1.00[ASW][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs1788988	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1944967	0.84[ASW][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs4121811	0.82[EUR][1000 genomes]
rs4447506	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs477256	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs484350	0.83[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4890222	0.91[EUR][1000 genomes]
rs500086	0.80[ASN][1000 genomes]
rs503472	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs511605	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs514227	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs515626	0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs519465	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525399	0.80[ASN][1000 genomes]
rs530113	0.80[ASN][1000 genomes]
rs531258	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs535626	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs559231	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs577955	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs582268	0.86[ASN][1000 genomes]
rs587686	0.82[ASN][1000 genomes]
rs593248	1.00[ASW][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs600658	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs620344	0.80[ASN][1000 genomes]
rs622939	0.80[ASN][1000 genomes]
rs627636	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs639656	0.80[ASN][1000 genomes]
rs647512	0.80[ASN][1000 genomes]
rs681048	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693020	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7237998	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv1067132	chr18:39691269-39808287	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
15	nsv543687	chr18:39691269-39808287	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs584380	PIK3C3	cis	parietal	SCAN
rs584380	PIK3C3	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39692200-39695600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr18:39692600-39694800	Enhancers	Fetal Intestine Small	intestine
3	chr18:39692800-39694000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr18:39692800-39694800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr18:39693000-39694200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr18:39693000-39695000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr18:39693200-39694000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr18:39693200-39694000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr18:39693200-39694200	Enhancers	Primary hematopoietic stem cells	blood
10	chr18:39693200-39694400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr18:39693200-39694400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr18:39693200-39694800	Enhancers	Dnd41	blood
13	chr18:39693400-39694000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr18:39693400-39694200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr18:39693400-39694200	Enhancers	K562	blood
16	chr18:39693400-39694400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:39693400-39694600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr18:39693400-39694600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr18:39693400-39694800	Enhancers	Colon Smooth Muscle	Colon
20	chr18:39693400-39694800	Enhancers	Fetal Intestine Large	intestine
21	chr18:39693400-39694800	Enhancers	Osteobl	bone
22	chr18:39693600-39694600	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr18:39693600-39694800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr18:39693800-39694000	Flanking Active TSS	HSMMtube	muscle
25	chr18:39693800-39694200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr18:39693800-39694200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr18:39693800-39694200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr18:39693800-39694200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:39693800-39694200	Enhancers	Duodenum Mucosa	Duodenum
30	chr18:39693800-39694200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr18:39693800-39694200	Flanking Active TSS	GM12878-XiMat	blood
32	chr18:39693800-39694400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:39693800-39694400	Enhancers	Primary B cells from peripheral blood	blood
34	chr18:39693800-39694400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr18:39693800-39694400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr18:39693800-39694400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr18:39693800-39694400	Enhancers	Brain Angular Gyrus	brain
38	chr18:39693800-39694400	Enhancers	Brain Cingulate Gyrus	brain
39	chr18:39693800-39694400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr18:39693800-39694400	Enhancers	Stomach Smooth Muscle	stomach
41	chr18:39693800-39694400	Enhancers	A549	lung
42	chr18:39693800-39694400	Flanking Active TSS	HepG2	liver
43	chr18:39693800-39694400	Enhancers	HMEC	breast
44	chr18:39693800-39694400	Enhancers	HSMM	muscle
45	chr18:39693800-39694400	Enhancers	NH-A	brain
46	chr18:39693800-39694400	Enhancers	NHDF-Ad	bronchial
47	chr18:39693800-39694600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr18:39693800-39694600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr18:39693800-39694600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr18:39693800-39694600	Enhancers	Primary T helper cells fromperipheralblood	blood

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