Variant report

Variant	rs66993340
Chromosome Location	chr9:97713973-97713974
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr9:97713153-97714045	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97705028..97708373-chr9:97712874..97716107,3	MCF-7	breast:
2	chr9:97713398..97716308-chr9:97717778..97720167,2	MCF-7	breast:
3	chr9:97702356..97704660-chr9:97713620..97715867,3	MCF-7	breast:
4	chr9:97682502..97684429-chr9:97713888..97715446,2	MCF-7	breast:
5	chr9:97711544..97713336-chr9:97713597..97715255,2	MCF-7	breast:
6	chr9:97712288..97714275-chr9:97755356..97757611,2	MCF-7	breast:
7	chr9:97711689..97714649-chr9:97733547..97735329,2	MCF-7	breast:
8	chr9:97711176..97714022-chr9:97766697..97771903,4	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10125566	0.81[AMR][1000 genomes]
rs10217441	0.81[AMR][1000 genomes]
rs10732407	0.81[AMR][1000 genomes]
rs10739988	0.81[AMR][1000 genomes]
rs10739990	0.81[AMR][1000 genomes]
rs10739991	0.84[AFR][1000 genomes]
rs10821411	0.81[AMR][1000 genomes]
rs1113967	0.81[AMR][1000 genomes]
rs12551506	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12552838	0.97[AMR][1000 genomes]
rs12554043	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12683896	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1382411	0.86[AMR][1000 genomes]
rs1382412	0.86[AMR][1000 genomes]
rs1542107	0.81[AMR][1000 genomes]
rs1571897	0.90[ASN][1000 genomes]
rs16911834	0.97[AMR][1000 genomes]
rs1904201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026399	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2095069	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2119953	0.81[AMR][1000 genomes]
rs2406897	0.81[AMR][1000 genomes]
rs2406898	0.81[AMR][1000 genomes]
rs2897523	0.81[AMR][1000 genomes]
rs3847311	0.84[AMR][1000 genomes]
rs3886568	0.81[AMR][1000 genomes]
rs41316526	0.86[AMR][1000 genomes]
rs4332191	0.81[AMR][1000 genomes]
rs4743976	0.90[ASN][1000 genomes]
rs4744389	0.81[AMR][1000 genomes]
rs6479581	0.81[AMR][1000 genomes]
rs66642068	0.86[AMR][1000 genomes]
rs66863985	0.86[AMR][1000 genomes]
rs67490803	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67756624	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7019602	0.81[AMR][1000 genomes]
rs7029570	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7044371	0.81[AMR][1000 genomes]
rs7046900	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72748601	0.97[AMR][1000 genomes]
rs72750335	0.81[EUR][1000 genomes]
rs72750346	0.81[EUR][1000 genomes]
rs73538177	0.86[AMR][1000 genomes]
rs7869736	0.81[AMR][1000 genomes]
rs894426	0.81[AMR][1000 genomes]
rs894427	0.81[AMR][1000 genomes]

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97685200-97714600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:97687000-97714000	Weak transcription	Thymus	Thymus
4	chr9:97700200-97714600	Weak transcription	Fetal Stomach	stomach
5	chr9:97700200-97718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:97708800-97714000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:97708800-97715000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:97708800-97720000	Weak transcription	K562	blood
9	chr9:97709200-97730400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:97710000-97715200	Enhancers	Ovary	ovary
11	chr9:97710000-97715600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:97710400-97715000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:97710600-97716000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr9:97710600-97716200	Enhancers	Left Ventricle	heart
15	chr9:97710600-97716800	Enhancers	Placenta	Placenta
16	chr9:97710800-97714200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr9:97710800-97715600	Genic enhancers	HSMM	muscle
18	chr9:97711200-97715800	Enhancers	Brain Anterior Caudate	brain
19	chr9:97711200-97715800	Enhancers	Brain Substantia Nigra	brain
20	chr9:97711200-97716200	Enhancers	Fetal Muscle Leg	muscle
21	chr9:97711200-97719000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:97711400-97714600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:97711400-97714800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:97711400-97717400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:97711600-97715800	Enhancers	Brain Hippocampus Middle	brain
26	chr9:97711800-97714600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:97711800-97715800	Enhancers	Brain Cingulate Gyrus	brain
28	chr9:97711800-97716800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr9:97712000-97715400	Enhancers	Right Ventricle	heart
30	chr9:97712000-97716000	Enhancers	HSMMtube	muscle
31	chr9:97712200-97715600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:97712400-97714200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:97712400-97714200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr9:97712400-97714800	Enhancers	HepG2	liver
35	chr9:97712400-97715000	Enhancers	Spleen	Spleen
36	chr9:97712400-97715400	Enhancers	Liver	Liver
37	chr9:97712400-97715400	Enhancers	Esophagus	oesophagus
38	chr9:97712400-97715400	Enhancers	Fetal Muscle Trunk	muscle
39	chr9:97712400-97715400	Enhancers	Pancreas	Pancrea
40	chr9:97712400-97715400	Enhancers	Right Atrium	heart
41	chr9:97712400-97715600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:97712400-97715600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97712400-97715600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:97712400-97715800	Enhancers	NHDF-Ad	bronchial
45	chr9:97712600-97714200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:97712600-97714200	Enhancers	Lung	lung
47	chr9:97712600-97714400	Enhancers	Stomach Mucosa	stomach
48	chr9:97712600-97714600	Enhancers	Gastric	stomach
49	chr9:97712600-97715000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:97712600-97715400	Enhancers	Adipose Nuclei	Adipose

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