Variant report

Variant	rs12683178
Chromosome Location	chr9:17579763-17579764
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10116876	0.80[ASN][1000 genomes]
rs10120378	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1028594	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10435770	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10756891	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10810810	0.92[ASN][1000 genomes]
rs10810811	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10810812	0.83[ASN][1000 genomes]
rs13294100	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2254582	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754341	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3758216	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758217	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780254	0.93[ASN][1000 genomes]
rs7022382	0.90[ASN][1000 genomes]
rs7028060	0.80[ASN][1000 genomes]
rs7029346	0.86[ASN][1000 genomes]
rs7030014	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7047611	0.83[ASN][1000 genomes]
rs7047709	0.85[ASN][1000 genomes]
rs7849043	0.80[ASN][1000 genomes]
rs7859530	0.80[ASN][1000 genomes]
rs7867956	0.80[ASN][1000 genomes]
rs8181077	0.83[EUR][1000 genomes];0.94[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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17577800-17580000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:17578200-17580000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:17578200-17580600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:17578400-17579800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr9:17578400-17580000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr9:17578400-17580000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr9:17578400-17580000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr9:17578400-17580000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:17578400-17580000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
10	chr9:17578400-17580200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr9:17578400-17580200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr9:17578400-17580400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr9:17578400-17580800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:17578400-17580800	Active TSS	Fetal Brain Female	brain
15	chr9:17578600-17579800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr9:17578600-17579800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:17578600-17579800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:17578600-17579800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
24	chr9:17578600-17579800	Bivalent Enhancer	Placenta	Placenta
25	chr9:17578600-17579800	Active TSS	Gastric	stomach
26	chr9:17578600-17579800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
27	chr9:17578600-17579800	Flanking Bivalent TSS/Enh	HMEC	breast
28	chr9:17578600-17579800	Bivalent/Poised TSS	HSMM	muscle
29	chr9:17578600-17579800	Bivalent/Poised TSS	NHEK	skin
30	chr9:17578600-17579800	Bivalent/Poised TSS	Osteobl	bone
31	chr9:17578600-17580000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr9:17578600-17580000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:17578600-17580000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:17578600-17580000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:17578600-17580000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:17578600-17580000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:17578600-17580000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
38	chr9:17578800-17579800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:17578800-17579800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:17578800-17579800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
41	chr9:17578800-17579800	Flanking Active TSS	Pancreas	Pancrea
42	chr9:17578800-17579800	Bivalent/Poised TSS	A549	lung
43	chr9:17578800-17580000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:17578800-17580000	Active TSS	Brain Substantia Nigra	brain
45	chr9:17578800-17580000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr9:17578800-17580200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:17578800-17580200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
48	chr9:17578800-17580400	Active TSS	Brain Angular Gyrus	brain
49	chr9:17578800-17580600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
50	chr9:17579000-17579800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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