Variant report

Variant	rs10992338
Chromosome Location	chr9:92704074-92704075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:92693505..92695699-chr9:92701901..92704107,2	MCF-7	breast:
2	chr9:92696162..92698839-chr9:92703402..92705829,2	MCF-7	breast:
3	chr9:92218435..92219998-chr9:92703276..92705546,2	MCF-7	breast:
4	chr9:92699147..92701279-chr9:92703484..92705697,2	K562	blood:
5	chr9:92687092..92689404-chr9:92701251..92704588,3	MCF-7	breast:
6	chr9:92702537..92704266-chr9:92708218..92709881,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10820884	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10820923	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821065	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821308	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821358	0.89[EUR][1000 genomes]
rs10821381	0.89[EUR][1000 genomes]
rs10992209	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992637	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993051	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993105	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993510	0.84[EUR][1000 genomes]
rs1155647	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319777	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1561948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1561949	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1561950	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1866766	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196921	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2196923	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2379196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7036596	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7466044	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7861478	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10992338	C9orf153	cis	cerebellum	SCAN
rs10992338	NFIL3	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92698200-92704400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:92701400-92704600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr9:92701600-92704800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:92701800-92704800	Enhancers	Pancreas	Pancrea
5	chr9:92701800-92705600	Enhancers	Ovary	ovary
6	chr9:92702200-92705200	Enhancers	Placenta	Placenta
7	chr9:92702800-92704800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:92702800-92705000	Enhancers	Fetal Heart	heart
9	chr9:92703000-92704600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:92703000-92704800	Enhancers	NHDF-Ad	bronchial
11	chr9:92703000-92704800	Enhancers	NHLF	lung
12	chr9:92703000-92705000	Enhancers	Left Ventricle	heart
13	chr9:92703000-92706000	Enhancers	HSMM	muscle
14	chr9:92703000-92706200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:92703000-92706400	Enhancers	Stomach Smooth Muscle	stomach
16	chr9:92703000-92707000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr9:92703200-92704200	Enhancers	Right Ventricle	heart
18	chr9:92703200-92704800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr9:92703200-92704800	Enhancers	Esophagus	oesophagus
20	chr9:92703200-92705000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:92703200-92705000	Enhancers	NH-A	brain
22	chr9:92703200-92705200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:92703200-92706000	Enhancers	HSMMtube	muscle
24	chr9:92703600-92704800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:92703600-92705000	Enhancers	Fetal Muscle Trunk	muscle
26	chr9:92703800-92704200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:92703800-92704200	Enhancers	Fetal Intestine Small	intestine
28	chr9:92703800-92704200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr9:92703800-92704400	Enhancers	Brain Germinal Matrix	brain
30	chr9:92703800-92704600	Enhancers	Rectal Smooth Muscle	rectum
31	chr9:92703800-92704800	Enhancers	Fetal Stomach	stomach
32	chr9:92703800-92705600	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr9:92703800-92705600	Enhancers	Placenta Amnion	Placenta Amnion
34	chr9:92703800-92705800	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr9:92703800-92707000	Enhancers	Psoas Muscle	Psoas
36	chr9:92703800-92709800	Enhancers	Colon Smooth Muscle	Colon
37	chr9:92704000-92704200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:92704000-92704600	Weak transcription	Aorta	Aorta
39	chr9:92704000-92704800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:92704000-92704800	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr9:92704000-92704800	Enhancers	Right Atrium	heart

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