Variant report

Variant	rs7039403
Chromosome Location	chr9:79449426-79449427
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	chr9:79448266..79451222-chr9:79453871..79455788,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10869833	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10869834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10869835	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10869837	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11145080	0.80[AMR][1000 genomes]
rs11145085	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12353019	0.80[AMR][1000 genomes]
rs1343394	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1936292	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2000288	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2000289	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744812	0.80[AMR][1000 genomes]
rs7022561	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7046472	0.80[AMR][1000 genomes]
rs7855857	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7861202	0.80[AMR][1000 genomes]
rs7867564	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758190	chr9:79365865-79673907	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759697	chr9:79365865-79673907	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79418400-79451000	Weak transcription	Fetal Stomach	stomach
2	chr9:79433200-79449800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:79433200-79449800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:79434200-79449800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:79435600-79455800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:79439600-79449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:79440800-79450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:79441200-79449800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:79441200-79450800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:79441400-79449600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:79441400-79461000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:79441600-79449600	Weak transcription	Aorta	Aorta
13	chr9:79441600-79449800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:79441800-79449600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:79443400-79449600	Weak transcription	HSMMtube	muscle
16	chr9:79444800-79449600	Weak transcription	Adipose Nuclei	Adipose
17	chr9:79445000-79449600	Weak transcription	Osteobl	bone
18	chr9:79449000-79449600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:79449000-79449600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:79449000-79450000	Enhancers	Colon Smooth Muscle	Colon
21	chr9:79449000-79452400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:79449000-79452600	Enhancers	Rectal Smooth Muscle	rectum
23	chr9:79449200-79449800	Enhancers	NHDF-Ad	bronchial
24	chr9:79449200-79449800	Enhancers	NHLF	lung
25	chr9:79449200-79450200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:79449200-79450200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr9:79449200-79451600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:79449200-79451600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:79449400-79449800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:79449400-79449800	Enhancers	HSMM	muscle
31	chr9:79449400-79451600	Enhancers	Brain Hippocampus Middle	brain
32	chr9:79449400-79451600	Enhancers	Brain Substantia Nigra	brain
33	chr9:79449400-79451800	Enhancers	NH-A	brain

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