Variant report

Variant	rs6477593
Chromosome Location	chr9:110494208-110494209
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	chr9:110251222..110252874-chr9:110493739..110495674,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136826	Chromatin interaction

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

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

rs_ID	r²[population]
rs1571572	0.89[EUR][1000 genomes]
rs2417804	0.85[CHD][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap]
rs6477595	0.87[ASN][1000 genomes]
rs7036850	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7044046	0.80[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
rs6477593	TMEM38B	cis	cerebellum	SCAN
rs6477593	C9orf152	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110482800-110495000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:110486800-110495400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:110490000-110494600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:110490000-110494600	Weak transcription	NHLF	lung
5	chr9:110490000-110495200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:110490200-110494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:110490200-110494400	Weak transcription	Osteobl	bone
8	chr9:110490200-110494600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:110490200-110494600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:110490200-110494600	Weak transcription	HSMM	muscle
11	chr9:110490200-110494800	Weak transcription	HUVEC	blood vessel
12	chr9:110490200-110495000	Weak transcription	NH-A	brain
13	chr9:110490200-110495200	Weak transcription	Aorta	Aorta
14	chr9:110490400-110494400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:110491800-110495200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:110492200-110495600	Enhancers	Fetal Muscle Leg	muscle
17	chr9:110492800-110496000	Enhancers	Fetal Muscle Trunk	muscle
18	chr9:110493200-110494800	Weak transcription	HSMMtube	muscle
19	chr9:110493200-110495000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:110493200-110495200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr9:110493800-110495400	Enhancers	Right Atrium	heart
22	chr9:110494000-110495000	Weak transcription	Psoas Muscle	Psoas
23	chr9:110494200-110494600	Enhancers	Pancreas	Pancrea
24	chr9:110494200-110495000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:110494200-110495200	Enhancers	Ovary	ovary
26	chr9:110494200-110495200	Enhancers	NHDF-Ad	bronchial
27	chr9:110494200-110495400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:110494200-110495600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:110494200-110497400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr9:110494200-110499200	Enhancers	Placenta	Placenta

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