Variant report

Variant	rs11716682
Chromosome Location	chr3:46651783-46651784
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	JUN	chr3:46651656-46651879	HepG2	liver:	n/a	chr3:46651726-46651739 chr3:46651679-46651688 chr3:46651679-46651686
2	CEBPB	chr3:46651655-46651840	Hela-S3	cervix:	n/a	chr3:46651729-46651740
3	JUND	chr3:46651605-46651874	HepG2	liver:	n/a	chr3:46651679-46651688 chr3:46651679-46651686
4	CEBPB	chr3:46651613-46651911	HepG2	liver:	n/a	chr3:46651729-46651740
5	CEBPB	chr3:46651546-46651888	IMR90	lung:	n/a	chr3:46651729-46651740
6	CEBPB	chr3:46651566-46651908	K562	blood:	n/a	chr3:46651729-46651740
7	GATA3	chr3:46651748-46652200	SH-SY5Y	brain:	n/a	n/a
8	GATA2	chr3:46651462-46652210	SH-SY5Y	brain:	n/a	chr3:46651677-46651686

Variant related genes	Relation type
TDGF1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11709309	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713702	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715694	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719804	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11919651	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs11929118	1.00[YRI][hapmap]
rs12486039	1.00[JPT][hapmap]
rs12639258	1.00[CHB][hapmap]
rs13327723	1.00[CHB][hapmap]
rs17221752	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62248664	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62248667	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441998	1.00[CHB][hapmap]
rs6792245	0.87[CEU][hapmap]
rs7644995	1.00[CHB][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876738	chr3:46639048-46680063	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46646200-46654000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:46648200-46652000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:46648200-46652000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:46648600-46652000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:46650400-46651800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:46650600-46652000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:46650600-46652000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:46650800-46651800	Bivalent Enhancer	NHEK	skin
9	chr3:46650800-46652000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr3:46650800-46652000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:46650800-46654600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:46651000-46652000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:46651000-46652600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:46651200-46652000	Enhancers	Fetal Lung	lung
15	chr3:46651200-46653400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:46651200-46653600	Weak transcription	Adipose Nuclei	Adipose
17	chr3:46651400-46651800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:46651400-46653400	Weak transcription	Liver	Liver
19	chr3:46651400-46653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:46651400-46654000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:46651400-46654200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:46651400-46655000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:46651400-46655400	Enhancers	Fetal Muscle Leg	muscle
24	chr3:46651600-46653000	Weak transcription	Placenta	Placenta
25	chr3:46651600-46653600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:46651600-46653800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:46651600-46655000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:46651600-46671200	Weak transcription	Right Atrium	heart

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