Variant report

Variant	rs6477595
Chromosome Location	chr9:110497436-110497437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:110493820..110495597-chr9:110496777..110499007,2	MCF-7	breast:
2	chr9:110496966..110498533-chr9:110500002..110502085,2	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11794132	1.00[ASW][hapmap]
rs2417804	0.90[JPT][hapmap];1.00[LWK][hapmap]
rs6477593	0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[ASN][1000 genomes]
rs6477596	0.81[JPT][hapmap]
rs7044046	0.90[JPT][hapmap]

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	nsv427850	chr9:110456613-110632324	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv428221	chr9:110456613-110632324	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6477595	TXN	cis	parietal	SCAN
rs6477595	OR13C3	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110494200-110499200	Enhancers	Placenta	Placenta
2	chr9:110494800-110497800	Enhancers	Fetal Stomach	stomach
3	chr9:110495200-110498800	Weak transcription	Lung	lung
4	chr9:110495200-110501800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:110495800-110504200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:110496000-110497600	Enhancers	NHEK	skin
7	chr9:110496000-110498600	Enhancers	HMEC	breast
8	chr9:110496000-110499000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:110496000-110499200	Enhancers	Fetal Muscle Leg	muscle
10	chr9:110496000-110500000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:110496000-110500400	Weak transcription	A549	lung
12	chr9:110496000-110500800	Weak transcription	Pancreas	Pancrea
13	chr9:110496000-110503200	Enhancers	Fetal Lung	lung
14	chr9:110496000-110503600	Enhancers	Ovary	ovary
15	chr9:110496000-110510800	Weak transcription	Aorta	Aorta
16	chr9:110496200-110497600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:110496200-110497600	Enhancers	Adipose Nuclei	Adipose
18	chr9:110496200-110497600	Enhancers	HSMM	muscle
19	chr9:110496200-110498800	Weak transcription	Left Ventricle	heart
20	chr9:110496200-110499000	Enhancers	Liver	Liver
21	chr9:110496200-110500000	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:110496200-110500000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr9:110496200-110500000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:110496200-110500000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:110496200-110500000	Weak transcription	Stomach Mucosa	stomach
26	chr9:110496200-110500200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:110496200-110500200	Weak transcription	Small Intestine	intestine
28	chr9:110496200-110500200	Enhancers	Hela-S3	cervix
29	chr9:110496200-110500800	Weak transcription	Brain Anterior Caudate	brain
30	chr9:110496200-110502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:110496200-110502400	Weak transcription	Gastric	stomach
32	chr9:110496200-110502400	Enhancers	Osteobl	bone
33	chr9:110496800-110497600	Enhancers	Fetal Muscle Trunk	muscle
34	chr9:110496800-110499200	Weak transcription	Spleen	Spleen
35	chr9:110496800-110500000	Weak transcription	NH-A	brain
36	chr9:110496800-110500200	Weak transcription	Colonic Mucosa	Colon
37	chr9:110496800-110501000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr9:110497000-110498600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:110497000-110499200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:110497000-110499600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:110497000-110500200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr9:110497000-110500200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:110497000-110503000	Enhancers	NHDF-Ad	bronchial
44	chr9:110497000-110503000	Enhancers	NHLF	lung
45	chr9:110497200-110497600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:110497200-110502000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:110497200-110502000	Weak transcription	Colon Smooth Muscle	Colon
48	chr9:110497200-110506600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr9:110497200-110506800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr9:110497400-110497600	Weak transcription	Esophagus	oesophagus

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