Variant report

Variant	rs9524380
Chromosome Location	chr13:94889033-94889034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1412934	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[ASN][1000 genomes]
rs1886930	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs4773782	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9301945	0.96[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs9516373	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9561517	0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv430599	chr13:94699399-94934930	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv933263	chr13:94711183-94897124	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv562754	chr13:94770794-94895346	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9524380	GPC6	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94886400-94891000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:94886400-94891000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr13:94886400-94891000	Weak transcription	HMEC	breast
4	chr13:94886400-94891200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr13:94886600-94890800	Weak transcription	NHDF-Ad	bronchial
6	chr13:94886600-94891200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:94886600-94892000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:94887200-94891000	Weak transcription	HSMMtube	muscle
9	chr13:94887200-94891400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:94888000-94890200	Enhancers	Fetal Intestine Small	intestine
11	chr13:94888200-94890200	Enhancers	Primary hematopoietic stem cells	blood
12	chr13:94888200-94890200	Enhancers	Fetal Intestine Large	intestine
13	chr13:94888400-94889600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:94888400-94890400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:94888400-94893600	Enhancers	Primary T cells from cord blood	blood
16	chr13:94888600-94889400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr13:94888600-94889400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr13:94888600-94889400	Enhancers	Osteobl	bone
19	chr13:94888600-94889600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:94888600-94889600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr13:94888600-94889800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr13:94888600-94890000	Enhancers	Primary B cells from peripheral blood	blood
23	chr13:94888600-94890200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr13:94888600-94892600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr13:94888600-94892600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr13:94888800-94889400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:94888800-94889400	Enhancers	Liver	Liver
28	chr13:94888800-94891800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr13:94889000-94889200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:94889000-94889200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr13:94889000-94889400	Enhancers	HSMM	muscle
32	chr13:94889000-94889400	Enhancers	NH-A	brain
33	chr13:94889000-94889800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr13:94889000-94890000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr13:94889000-94890000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:94889000-94892200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr13:94889000-94892600	Enhancers	Fetal Thymus	thymus

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