Variant report

Variant	rs12001098
Chromosome Location	chr9:110407586-110407587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12347544	0.81[EUR][1000 genomes]
rs12347609	0.81[EUR][1000 genomes]
rs12347622	0.81[EUR][1000 genomes]
rs1523779	1.00[JPT][hapmap]
rs28379887	0.85[EUR][1000 genomes]
rs28410234	0.85[EUR][1000 genomes]
rs28501144	0.83[EUR][1000 genomes]
rs28545042	0.85[EUR][1000 genomes]
rs28558750	0.85[EUR][1000 genomes]
rs28718553	0.85[EUR][1000 genomes]
rs28756961	0.85[EUR][1000 genomes]
rs41368853	0.84[EUR][1000 genomes]
rs55732410	0.83[EUR][1000 genomes]
rs57223814	0.88[EUR][1000 genomes]
rs58725849	0.85[EUR][1000 genomes]
rs60233772	0.83[EUR][1000 genomes]
rs7341759	0.90[EUR][1000 genomes]
rs7341900	0.92[EUR][1000 genomes]
rs73653618	0.83[EUR][1000 genomes]
rs7847530	1.00[JPT][hapmap]
rs7875152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs940291	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv831683	chr9:110275212-110461288	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893700	chr9:110365337-110451516	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv528269	chr9:110402957-110410888	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12001098	ACTL7A	cis	cerebellum	SCAN
rs12001098	TAL2	cis	parietal	SCAN
rs12001098	OR13C9	cis	cerebellum	SCAN
rs12001098	NIPSNAP3A	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110401400-110407600	Weak transcription	Psoas Muscle	Psoas
2	chr9:110401600-110410000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:110402000-110407600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr9:110406200-110408800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr9:110406800-110407800	Enhancers	Fetal Muscle Trunk	muscle
6	chr9:110406800-110407800	Enhancers	Fetal Thymus	thymus
7	chr9:110406800-110408000	Enhancers	Fetal Muscle Leg	muscle
8	chr9:110406800-110408000	Enhancers	Placenta	Placenta
9	chr9:110406800-110408000	Enhancers	Left Ventricle	heart
10	chr9:110406800-110408200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr9:110407000-110407800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:110407000-110408000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr9:110407000-110408000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr9:110407000-110408000	Enhancers	Liver	Liver
15	chr9:110407000-110408000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr9:110407000-110408200	Enhancers	HUVEC	blood vessel
17	chr9:110407200-110407800	Enhancers	Brain Anterior Caudate	brain
18	chr9:110407200-110407800	Enhancers	Fetal Stomach	stomach
19	chr9:110407200-110408000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:110407200-110408200	Enhancers	Adipose Nuclei	Adipose
21	chr9:110407400-110407600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:110407400-110407600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:110407400-110407600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:110407400-110407600	Enhancers	HSMM	muscle
25	chr9:110407400-110407600	Enhancers	NHDF-Ad	bronchial
26	chr9:110407400-110407800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:110407400-110407800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:110407400-110407800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:110407400-110407800	Enhancers	Brain Cingulate Gyrus	brain
30	chr9:110407400-110407800	Enhancers	Brain Substantia Nigra	brain
31	chr9:110407400-110407800	Enhancers	Ovary	ovary
32	chr9:110407400-110408000	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:110407400-110408000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:110407400-110408000	Enhancers	Brain Angular Gyrus	brain
35	chr9:110407400-110408000	Enhancers	Brain Hippocampus Middle	brain
36	chr9:110407400-110408000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr9:110407400-110408000	Enhancers	Fetal Lung	lung
38	chr9:110407400-110408000	Enhancers	Lung	lung
39	chr9:110407400-110408000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr9:110407400-110408000	Enhancers	Right Atrium	heart
41	chr9:110407400-110408000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr9:110407400-110408000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr9:110407400-110408000	Bivalent Enhancer	Small Intestine	intestine
44	chr9:110407400-110408000	Enhancers	Stomach Mucosa	stomach
45	chr9:110407400-110408200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr9:110407400-110408200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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