Variant report

Variant	rs11788333
Chromosome Location	chr9:116094720-116094721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116087670..116090611-chr9:116094094..116096004,2	MCF-7	breast:
2	chr9:116093601..116095612-chr9:116137576..116139451,2	MCF-7	breast:
3	chr9:116094633..116097880-chr9:116104158..116105941,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119431	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10817478	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10817483	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10817484	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10981730	0.87[AFR][1000 genomes]
rs10981735	0.87[AFR][1000 genomes]
rs10981764	0.83[AFR][1000 genomes]
rs11787602	0.93[AFR][1000 genomes]
rs11791027	0.85[ASN][1000 genomes]
rs12378096	0.85[AFR][1000 genomes]
rs4979235	0.91[EUR][1000 genomes]
rs4979237	0.84[AFR][1000 genomes]
rs4979238	0.84[AFR][1000 genomes]
rs66747389	0.83[AFR][1000 genomes]
rs66790147	0.87[AFR][1000 genomes]
rs7025262	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7026114	0.87[AFR][1000 genomes]
rs7026831	0.87[AFR][1000 genomes]
rs7029469	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7038589	0.87[AFR][1000 genomes]
rs7870848	1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs912247	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][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
rs11788333	HDHD3	cis	Artery Tibial	GTEx

Chromatin state (count:42 , 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	chr9:116080800-116101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:116080800-116101600	Weak transcription	Fetal Brain Male	brain
7	chr9:116081000-116101600	Weak transcription	Pancreas	Pancrea
8	chr9:116081400-116098000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:116082200-116101600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:116082600-116101400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:116082800-116101400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:116082800-116101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:116082800-116101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:116082800-116101600	Weak transcription	Brain Substantia Nigra	brain
15	chr9:116082800-116101600	Weak transcription	Fetal Kidney	kidney
16	chr9:116082800-116101600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:116082800-116102000	Weak transcription	Aorta	Aorta
18	chr9:116083000-116101400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:116083800-116101200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:116083800-116101200	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:116083800-116101400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:116083800-116101600	Weak transcription	Right Ventricle	heart
23	chr9:116084000-116101400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:116084200-116101200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:116084200-116101400	Weak transcription	Liver	Liver
26	chr9:116084200-116101400	Weak transcription	Brain Anterior Caudate	brain
27	chr9:116084200-116101400	Weak transcription	Fetal Stomach	stomach
28	chr9:116084200-116101600	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:116085400-116101400	Weak transcription	Adipose Nuclei	Adipose
30	chr9:116085400-116101400	Weak transcription	Fetal Lung	lung
31	chr9:116085400-116101600	Weak transcription	Brain Angular Gyrus	brain
32	chr9:116085600-116101200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:116091400-116101400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:116092000-116101400	Weak transcription	Small Intestine	intestine
35	chr9:116093000-116101400	Weak transcription	Fetal Intestine Small	intestine
36	chr9:116093000-116101800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr9:116093600-116101200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr9:116094400-116097800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:116094400-116101200	Weak transcription	Left Ventricle	heart
40	chr9:116094400-116101400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:116094400-116101600	Weak transcription	Ovary	ovary
42	chr9:116094600-116095000	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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