Variant report

Variant	rs9588089
Chromosome Location	chr13:110745743-110745744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:110742841..110744367-chr13:110745194..110747379,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11069823	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348619	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373748	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975324	0.82[ASN][1000 genomes]
rs1816885	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166209	0.82[ASN][1000 genomes]
rs34870648	0.83[ASN][1000 genomes]
rs56206251	0.83[ASN][1000 genomes]
rs9588084	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9588091	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9588092	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3442659	chr13:110711145-110747162	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	esv3425970	chr13:110711165-110747132	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv563095	chr13:110724710-110761521	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv901005	chr13:110733102-110766350	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv515849	chr13:110742197-110761521	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv456111	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv456112	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv456113	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv563096	chr13:110742197-110761521	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv563097	chr13:110742197-110766350	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv456114	chr13:110742919-110761521	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv563098	chr13:110742919-110761521	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110738800-110746400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:110742000-110746800	Weak transcription	Liver	Liver
3	chr13:110742400-110746600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:110743400-110746400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr13:110744800-110746400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:110745000-110746000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:110745000-110746800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr13:110745200-110745800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:110745200-110746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:110745200-110747400	Enhancers	Right Ventricle	heart
11	chr13:110745200-110747600	Enhancers	Rectal Smooth Muscle	rectum
12	chr13:110745200-110747800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr13:110745200-110747800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr13:110745200-110749000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr13:110745400-110746000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:110745400-110746400	Enhancers	Colon Smooth Muscle	Colon
17	chr13:110745400-110747800	Enhancers	Right Atrium	heart
18	chr13:110745400-110749200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:110745600-110745800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:110745600-110745800	Weak transcription	HMEC	breast
21	chr13:110745600-110746000	Weak transcription	Brain Substantia Nigra	brain
22	chr13:110745600-110746000	Enhancers	Psoas Muscle	Psoas
23	chr13:110745600-110747200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:110745600-110748400	Enhancers	Pancreas	Pancrea

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