Variant report

Variant	rs3759452
Chromosome Location	chr13:92050403-92050404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr13:92050327-92050594	GM12878	blood:	n/a	n/a
2	IRF1	chr13:92050184-92051070	K562	blood:	n/a	chr13:92051029-92051043
3	JUND	chr13:92050197-92051318	K562	blood:	n/a	n/a
4	ZMIZ1	chr13:92050062-92051285	K562	blood:	n/a	n/a
5	GATA3	chr13:92050251-92050474	SH-SY5Y	brain:	n/a	chr13:92050272-92050289 chr13:92050308-92050324 chr13:92050276-92050297 chr13:92050306-92050327 chr13:92050278-92050294
6	ZNF143	chr13:92050178-92050894	K562	blood:	n/a	n/a
7	STAT5A	chr13:92050063-92050814	K562	blood:	n/a	chr13:92050542-92050550 chr13:92050098-92050106
8	MYC	chr13:92050321-92050900	K562	blood:	n/a	n/a
9	ZC3H11A	chr13:92049717-92051180	K562	blood:	n/a	n/a
10	MYC	chr13:92050371-92051081	K562	blood:	n/a	n/a
11	BHLHE40	chr13:92050364-92050903	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:92050067..92050884-chr13:92058646..92059591,2	K562	blood:

Variant related genes	Relation type
GPC5	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1330065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2147190	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4284505	0.84[GIH][hapmap]
rs7322734	0.84[GIH][hapmap]
rs7325533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7983063	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9515921	0.97[ASN][1000 genomes]
rs9523304	0.84[GIH][hapmap]
rs9523312	0.86[GIH][hapmap]
rs9523321	0.96[ASN][1000 genomes]
rs9523326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv1049382	chr13:92024240-92521180	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv541873	chr13:92024240-92521180	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3759452	GPC5	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92049800-92050600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
2	chr13:92050200-92050600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
3	chr13:92050200-92050600	Enhancers	Colon Smooth Muscle	Colon
4	chr13:92050200-92050600	Flanking Active TSS	GM12878-XiMat	blood
5	chr13:92050200-92050800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
6	chr13:92050200-92051200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr13:92050200-92052600	Active TSS	Brain Cingulate Gyrus	brain
8	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
10	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
11	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:92050400-92050600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr13:92050400-92050600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr13:92050400-92050600	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr13:92050400-92050600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
18	chr13:92050400-92050600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:92050400-92050600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr13:92050400-92050600	Bivalent Enhancer	Liver	Liver
21	chr13:92050400-92050600	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr13:92050400-92050600	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr13:92050400-92050600	Bivalent Enhancer	Brain Germinal Matrix	brain
24	chr13:92050400-92050600	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr13:92050400-92050600	Enhancers	Duodenum Mucosa	Duodenum
26	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	Fetal Heart	heart
27	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
28	chr13:92050400-92050600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr13:92050400-92050600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
30	chr13:92050400-92050600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr13:92050400-92050600	Active TSS	Right Atrium	heart
32	chr13:92050400-92050600	Bivalent Enhancer	A549	lung
33	chr13:92050400-92050600	Flanking Active TSS	Hela-S3	cervix
34	chr13:92050400-92050600	Enhancers	HepG2	liver
35	chr13:92050400-92050600	Bivalent Enhancer	HUVEC	blood vessel
36	chr13:92050400-92050600	Enhancers	Osteobl	bone
37	chr13:92050400-92050800	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
38	chr13:92050400-92050800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr13:92050400-92050800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr13:92050400-92050800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
41	chr13:92050400-92050800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr13:92050400-92050800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr13:92050400-92050800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr13:92050400-92050800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
45	chr13:92050400-92050800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:92050400-92050800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
47	chr13:92050400-92050800	Bivalent/Poised TSS	NHDF-Ad	bronchial
48	chr13:92050400-92051000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr13:92050400-92051000	Bivalent Enhancer	Adipose Nuclei	Adipose
50	chr13:92050400-92051000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle

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