Variant report

Variant	rs11790496
Chromosome Location	chr9:2572011-2572012
allele	A/T
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	GATA3	chr9:2571657-2572014	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236404	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10491719	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11795324	1.00[ASN][1000 genomes]
rs1512715	1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907952	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17422851	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17488771	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs472467	0.90[ASN][1000 genomes]
rs491525	0.90[ASN][1000 genomes]
rs522794	0.90[ASN][1000 genomes]
rs569020	0.90[ASN][1000 genomes]
rs588933	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs619976	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs620879	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs622667	1.00[JPT][hapmap]
rs622668	1.00[JPT][hapmap]
rs633334	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs633710	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs633757	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs656414	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs667091	0.90[ASN][1000 genomes]
rs73378869	1.00[ASN][1000 genomes]
rs7847026	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs829970	0.90[ASN][1000 genomes]
rs829971	1.00[JPT][hapmap]
rs829972	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs829973	0.90[ASN][1000 genomes]
rs9695107	0.90[ASN][1000 genomes]
rs9695842	0.90[ASN][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	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv466081	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv613132	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv892066	chr9:2397564-2589739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1033424	chr9:2508296-2575408	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv892068	chr9:2543888-2589739	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2559800-2577000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:2567600-2577600	Enhancers	Fetal Heart	heart
3	chr9:2568600-2576000	Enhancers	Ovary	ovary
4	chr9:2569000-2572400	Weak transcription	Left Ventricle	heart
5	chr9:2569000-2575400	Weak transcription	Right Ventricle	heart
6	chr9:2571000-2573200	Enhancers	Right Atrium	heart
7	chr9:2571000-2574200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:2571200-2573200	Enhancers	Psoas Muscle	Psoas
9	chr9:2571400-2573200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr9:2571400-2574000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:2571400-2574200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:2571400-2574400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:2571400-2576600	Weak transcription	Brain Substantia Nigra	brain
14	chr9:2571400-2576600	Weak transcription	Fetal Stomach	stomach
15	chr9:2571600-2573200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr9:2571600-2574200	Weak transcription	NHEK	skin
17	chr9:2571600-2575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:2571600-2576000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:2571600-2576600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:2571600-2576800	Weak transcription	Fetal Kidney	kidney
21	chr9:2571800-2574000	Weak transcription	HMEC	breast
22	chr9:2571800-2574400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:2571800-2574400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:2571800-2574400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:2571800-2574400	Weak transcription	Adipose Nuclei	Adipose
26	chr9:2572000-2572400	Weak transcription	Fetal Lung	lung
27	chr9:2572000-2574000	Weak transcription	Hela-S3	cervix
28	chr9:2572000-2574200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:2572000-2575800	Weak transcription	Rectal Mucosa Donor 31	rectum

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