Variant report

Variant	rs62562984
Chromosome Location	chr9:98707257-98707258
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11794391	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12684118	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12684321	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359916	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088294	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3824492	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742791	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743429	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60399336	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs963150	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62562984	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
3	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
4	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
7	chr9:98686400-98709000	Weak transcription	Right Ventricle	heart
8	chr9:98686400-98711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:98687800-98709000	Weak transcription	Lung	lung
11	chr9:98687800-98718400	Weak transcription	Stomach Mucosa	stomach
12	chr9:98687800-98726000	Weak transcription	Gastric	stomach
13	chr9:98690600-98709800	Weak transcription	HMEC	breast
14	chr9:98694600-98708400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr9:98695600-98718200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:98695800-98709200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:98695800-98742400	Weak transcription	NHLF	lung
18	chr9:98696200-98709600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:98697800-98713200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:98698800-98709200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:98699400-98709000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:98699400-98709600	Weak transcription	Brain Substantia Nigra	brain
23	chr9:98699600-98708400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:98699600-98717600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:98699800-98718600	Weak transcription	NHEK	skin
26	chr9:98701600-98709000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:98702400-98709200	Weak transcription	Fetal Stomach	stomach
28	chr9:98702400-98718600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:98702400-98718600	Weak transcription	Small Intestine	intestine
30	chr9:98702600-98707800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr9:98702600-98708400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:98702600-98709000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:98702600-98709000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr9:98702600-98709400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:98702600-98718600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:98702600-98718600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:98702600-98718600	Weak transcription	Aorta	Aorta
38	chr9:98702600-98718600	Weak transcription	Pancreas	Pancrea
39	chr9:98703600-98709000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:98703600-98709400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:98704000-98709000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr9:98704000-98714200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:98704200-98708400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:98704400-98709000	Weak transcription	Brain Angular Gyrus	brain
45	chr9:98704600-98709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:98704600-98709000	Weak transcription	Left Ventricle	heart
47	chr9:98704600-98709000	Weak transcription	Ovary	ovary
48	chr9:98704600-98709000	Weak transcription	Thymus	Thymus
49	chr9:98704600-98709200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:98704600-98709200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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