Variant report

Variant	rs10739406
Chromosome Location	chr9:116945547-116945548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116940464..116942565-chr9:116943951..116946533,3	K562	blood:
2	chr9:116938018..116940765-chr9:116944712..116947136,2	K562	blood:
3	chr9:116943873..116946561-chr9:116991422..116993679,2	MCF-7	breast:
4	chr9:116942707..116945654-chr9:116999630..117002329,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10759688	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431819	0.96[ASN][1000 genomes]
rs2567704	0.92[ASN][1000 genomes]
rs2808792	0.81[ASN][1000 genomes]
rs4979347	0.96[ASN][1000 genomes]
rs4979349	0.96[ASN][1000 genomes]
rs4979351	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
5	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
6	nsv466532	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv615232	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
9	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
10	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10739406	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116919200-116972000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:116926400-116950200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:116926400-116950400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:116930600-116954400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:116931000-116946400	Genic enhancers	Fetal Stomach	stomach
6	chr9:116931000-116971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:116932800-116971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:116935000-116946600	Enhancers	Liver	Liver
9	chr9:116938000-116956200	Weak transcription	Gastric	stomach
10	chr9:116939200-116948800	Weak transcription	Brain Germinal Matrix	brain
11	chr9:116939400-116967200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:116940200-116950000	Genic enhancers	Fetal Muscle Leg	muscle
13	chr9:116940400-116946200	Weak transcription	Hela-S3	cervix
14	chr9:116940400-116965200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:116940600-116946800	Weak transcription	A549	lung
16	chr9:116940600-116947800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:116940600-116955800	Weak transcription	HMEC	breast
18	chr9:116940800-116945600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:116941200-116946400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:116941400-116950800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:116941600-116946800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:116941600-116965600	Weak transcription	Osteobl	bone
23	chr9:116941800-116946000	Weak transcription	Spleen	Spleen
24	chr9:116941800-116952600	Weak transcription	Esophagus	oesophagus
25	chr9:116941800-116962800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:116942800-116951200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:116943400-116966800	Weak transcription	Fetal Thymus	thymus
28	chr9:116943600-116968400	Weak transcription	Stomach Mucosa	stomach
29	chr9:116943800-116948200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:116944000-116946600	Weak transcription	Right Ventricle	heart
31	chr9:116944000-116948600	Weak transcription	Lung	lung
32	chr9:116944000-116948800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr9:116944000-116950400	Strong transcription	Fetal Intestine Small	intestine
34	chr9:116944000-116952000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:116944000-116966600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:116944200-116946400	Weak transcription	HUVEC	blood vessel
37	chr9:116944200-116947400	Weak transcription	Brain Substantia Nigra	brain
38	chr9:116944200-116950200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:116944200-116950400	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:116944200-116950600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:116944200-116950800	Strong transcription	Fetal Intestine Large	intestine
42	chr9:116944200-116950800	Strong transcription	NHEK	skin
43	chr9:116944200-116952200	Weak transcription	HSMM	muscle
44	chr9:116944200-116954400	Weak transcription	Psoas Muscle	Psoas
45	chr9:116944200-116960000	Weak transcription	NHDF-Ad	bronchial
46	chr9:116944200-116962800	Weak transcription	NH-A	brain
47	chr9:116944200-116965600	Strong transcription	HepG2	liver
48	chr9:116944200-116967200	Weak transcription	Aorta	Aorta
49	chr9:116944200-116967400	Weak transcription	Right Atrium	heart
50	chr9:116944200-116969200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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