Variant report

Variant	rs13440240
Chromosome Location	chr9:12923693-12923694
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	chr9:12922589..12925309-chr9:12932316..12933934,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10122098	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125252	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10511575	0.85[ASN][1000 genomes]
rs12338576	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12708253	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13440325	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1984049	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1984050	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1984051	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28545148	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28638037	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34392930	0.92[EUR][1000 genomes]
rs35873446	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7847454	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7870401	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv613615	chr9:12830070-12947238	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv613616	chr9:12922330-13018096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13440240	C9orf150	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12917000-12933600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr9:12917200-12930000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:12917200-12934000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:12917400-12933600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:12922000-12925400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:12922200-12924800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:12922200-12924800	Enhancers	Fetal Heart	heart
8	chr9:12922200-12925400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:12922200-12925400	Enhancers	NHDF-Ad	bronchial
10	chr9:12922400-12924000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:12922600-12924000	Enhancers	Fetal Stomach	stomach
12	chr9:12922600-12924200	Enhancers	Adipose Nuclei	Adipose
13	chr9:12922800-12923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:12922800-12923800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:12922800-12931000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:12923000-12924800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:12923200-12924000	Enhancers	HSMMtube	muscle
18	chr9:12923200-12924200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:12923200-12924200	Enhancers	Aorta	Aorta
20	chr9:12923200-12924200	Enhancers	Right Atrium	heart
21	chr9:12923200-12924200	Enhancers	HMEC	breast
22	chr9:12923200-12924400	Enhancers	NHLF	lung
23	chr9:12923200-12924400	Enhancers	Osteobl	bone
24	chr9:12923200-12925400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:12923200-12925400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:12923400-12923800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:12923400-12924000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:12923400-12924000	Enhancers	Colon Smooth Muscle	Colon
29	chr9:12923400-12924000	Enhancers	Fetal Lung	lung
30	chr9:12923400-12924200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr9:12923400-12924200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:12923400-12924200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr9:12923400-12924200	Enhancers	Right Ventricle	heart
34	chr9:12923400-12924200	Enhancers	NH-A	brain
35	chr9:12923400-12924800	Enhancers	HSMM	muscle

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