Variant report

Variant	rs9596095
Chromosome Location	chr13:49974615-49974616
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	chr13:49971896..49974860-chr13:49997349..49999388,2	MCF-7	breast:
2	chr13:49961570..49963263-chr13:49972646..49974956,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11148144	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2146398	0.95[CEU][hapmap]
rs9285172	0.95[CEU][hapmap]
rs9316445	1.00[CHB][hapmap]
rs9526554	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9596095	CAB39L	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49970000-49975000	Weak transcription	NHDF-Ad	bronchial
2	chr13:49970000-49975200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr13:49970400-49975200	Weak transcription	Osteobl	bone
4	chr13:49970600-49975200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:49971800-49976400	Active TSS	Stomach Smooth Muscle	stomach
6	chr13:49972000-49975800	Active TSS	Adipose Nuclei	Adipose
7	chr13:49972000-49976400	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr13:49972200-49976000	Active TSS	Right Atrium	heart
9	chr13:49972200-49976400	Active TSS	Aorta	Aorta
10	chr13:49972800-49976000	Active TSS	Brain Anterior Caudate	brain
11	chr13:49972800-49976000	Active TSS	Ovary	ovary
12	chr13:49972800-49976000	Active TSS	Rectal Smooth Muscle	rectum
13	chr13:49973000-49975800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr13:49973000-49976000	Active TSS	Brain Hippocampus Middle	brain
15	chr13:49973200-49976000	Active TSS	Brain Substantia Nigra	brain
16	chr13:49973400-49975600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:49973400-49976000	Active TSS	Colon Smooth Muscle	Colon
18	chr13:49973600-49975000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:49973600-49975000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr13:49973800-49975000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr13:49974000-49975200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr13:49974000-49975800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr13:49974000-49976200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:49974200-49975200	Active TSS	Duodenum Mucosa	Duodenum
25	chr13:49974200-49975200	Weak transcription	Fetal Intestine Small	intestine
26	chr13:49974200-49975400	Active TSS	Fetal Kidney	kidney
27	chr13:49974200-49975800	Active TSS	Fetal Stomach	stomach
28	chr13:49974200-49976000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr13:49974200-49976000	Active TSS	Brain Angular Gyrus	brain
30	chr13:49974200-49976000	Active TSS	Brain Cingulate Gyrus	brain
31	chr13:49974200-49976000	Active TSS	Fetal Heart	heart
32	chr13:49974400-49974800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr13:49974400-49975200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:49974400-49975200	Weak transcription	Right Ventricle	heart
35	chr13:49974600-49974800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr13:49974600-49975200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr13:49974600-49975800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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