Variant report

Variant	rs12005901
Chromosome Location	chr9:15233478-15233479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr9:15233289-15233814	GM12878	blood:	n/a	n/a
2	PAX5	chr9:15233324-15233699	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TTC39B	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10121353	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337646	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12341643	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12347380	1.00[AMR][1000 genomes]
rs28729420	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs525147	0.83[AMR][1000 genomes]
rs535659	0.83[AMR][1000 genomes]
rs548264	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv521191	chr9:15218947-15246652	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2761504	chr9:15227680-15237785	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr9:15193400-15249600	Weak transcription	Colonic Mucosa	Colon
2	chr9:15221200-15242200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:15221800-15242800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:15223400-15258200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr9:15223800-15235200	Weak transcription	Fetal Lung	lung
6	chr9:15224400-15242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:15224600-15235200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr9:15224600-15243600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:15224600-15244400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:15224800-15235000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:15229800-15235000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:15229800-15240000	Weak transcription	Aorta	Aorta
13	chr9:15229800-15243000	Weak transcription	Gastric	stomach
14	chr9:15229800-15243000	Weak transcription	Ovary	ovary
15	chr9:15230000-15235200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:15230000-15235200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr9:15230600-15235200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:15232000-15244400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:15232200-15233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:15232600-15233600	ZNF genes & repeats	Fetal Stomach	stomach
21	chr9:15232600-15235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:15232600-15246400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:15232800-15235200	Weak transcription	Primary T cells from cord blood	blood
24	chr9:15233000-15235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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