Variant report

Variant	rs12339006
Chromosome Location	chr9:116090874-116090875
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116089769..116092357-chr9:116100881..116102829,2	MCF-7	breast:
2	chr9:116088605..116091478-chr9:116091736..116093633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148225	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10114352	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10118304	0.85[AMR][1000 genomes]
rs10120336	0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10122035	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10481672	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10481673	0.85[AMR][1000 genomes]
rs10481675	0.90[YRI][hapmap];0.85[AMR][1000 genomes]
rs10981753	0.85[AMR][1000 genomes]
rs12336439	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337069	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337123	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12346510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12347798	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12348236	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12348581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12350255	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12350332	0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12350377	0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12352852	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12352895	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28375224	0.85[AMR][1000 genomes]
rs28393902	0.85[AMR][1000 genomes]
rs28488898	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28536744	0.85[AMR][1000 genomes]
rs28597401	0.85[AMR][1000 genomes]
rs28725394	0.85[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12339006	WDR31	cis	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
3	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:116077800-116101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:116078800-116093600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:116079000-116094600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:116080800-116101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:116080800-116101600	Weak transcription	Fetal Brain Male	brain
9	chr9:116081000-116101600	Weak transcription	Pancreas	Pancrea
10	chr9:116081400-116098000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:116082200-116101600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:116082600-116101400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:116082800-116101400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:116082800-116101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:116082800-116101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:116082800-116101600	Weak transcription	Brain Substantia Nigra	brain
17	chr9:116082800-116101600	Weak transcription	Fetal Kidney	kidney
18	chr9:116082800-116101600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:116082800-116102000	Weak transcription	Aorta	Aorta
20	chr9:116083000-116101400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:116083800-116093600	Weak transcription	Ovary	ovary
22	chr9:116083800-116094000	Weak transcription	Left Ventricle	heart
23	chr9:116083800-116101200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:116083800-116101200	Weak transcription	Colon Smooth Muscle	Colon
25	chr9:116083800-116101400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:116083800-116101600	Weak transcription	Right Ventricle	heart
27	chr9:116084000-116093600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:116084000-116101400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:116084200-116101200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:116084200-116101400	Weak transcription	Liver	Liver
31	chr9:116084200-116101400	Weak transcription	Brain Anterior Caudate	brain
32	chr9:116084200-116101400	Weak transcription	Fetal Stomach	stomach
33	chr9:116084200-116101600	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:116085400-116092000	Weak transcription	HSMMtube	muscle
35	chr9:116085400-116101400	Weak transcription	Adipose Nuclei	Adipose
36	chr9:116085400-116101400	Weak transcription	Fetal Lung	lung
37	chr9:116085400-116101600	Weak transcription	Brain Angular Gyrus	brain
38	chr9:116085600-116101200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:116086400-116092600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:116090400-116091400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:116090400-116091600	Enhancers	Fetal Intestine Small	intestine

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