Variant report

Variant	rs3758217
Chromosome Location	chr9:17578502-17578503
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	E2F6	chr9:17578483-17579540	H1-hESC	embryonic stem cell:	n/a	chr9:17579058-17579067 chr9:17579359-17579369 chr9:17579473-17579482 chr9:17578852-17578862 chr9:17579060-17579069

Variant related genes	Relation type
SH3GL2	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10113874	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10120378	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1022718	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1028594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10435770	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756891	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10810810	0.97[ASN][1000 genomes]
rs10810811	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810812	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12683178	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13294100	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2180905	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2254582	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2383031	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2593392	0.82[ASN][1000 genomes]
rs2754341	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3758216	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3808772	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3808775	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3808776	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4590535	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4961575	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7022382	0.90[ASN][1000 genomes]
rs7029346	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7030014	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7047611	0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7047709	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7859530	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7867956	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs8181077	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv517380	chr9:17564267-17633232	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466274	chr9:17564267-17633232	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv613701	chr9:17564267-17633232	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv892672	chr9:17564267-17634566	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1025072	chr9:17577141-17632543	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3414236	chr9:17577977-17580825	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17577800-17580000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:17578200-17578600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
3	chr9:17578200-17578600	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
4	chr9:17578200-17578600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
5	chr9:17578200-17578600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:17578200-17578800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
7	chr9:17578200-17579000	Bivalent/Poised TSS	Ovary	ovary
8	chr9:17578200-17580000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:17578200-17580600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr9:17578400-17578600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
11	chr9:17578400-17578600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:17578400-17578600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
13	chr9:17578400-17578600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:17578400-17578600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:17578400-17578600	Bivalent Enhancer	Adipose Nuclei	Adipose
16	chr9:17578400-17578600	Enhancers	Brain Hippocampus Middle	brain
17	chr9:17578400-17578600	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr9:17578400-17578600	Enhancers	Brain Substantia Nigra	brain
19	chr9:17578400-17578600	Bivalent Enhancer	Fetal Kidney	kidney
20	chr9:17578400-17578600	Bivalent Enhancer	Fetal Lung	lung
21	chr9:17578400-17578600	Enhancers	Right Ventricle	heart
22	chr9:17578400-17578600	Bivalent Enhancer	HUVEC	blood vessel
23	chr9:17578400-17579000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
24	chr9:17578400-17579000	Flanking Active TSS	Hela-S3	cervix
25	chr9:17578400-17579800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr9:17578400-17580000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr9:17578400-17580000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr9:17578400-17580000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr9:17578400-17580000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:17578400-17580000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
31	chr9:17578400-17580200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr9:17578400-17580200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr9:17578400-17580400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr9:17578400-17580800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:17578400-17580800	Active TSS	Fetal Brain Female	brain

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