Variant report

Variant	rs10817478
Chromosome Location	chr9:116078520-116078521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116076424..116079127-chr9:116102528..116104331,2	MCF-7	breast:
2	chr9:116071625..116073462-chr9:116076376..116079141,2	K562	blood:
3	chr9:116076058..116079132-chr9:116081074..116084162,3	K562	blood:
4	chr9:116077143..116079692-chr9:116110149..116111989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119411	Chromatin interaction
ENSG00000148225	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10817483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10817484	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981723	0.87[CHD][hapmap]
rs11788333	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4979235	0.92[EUR][1000 genomes]
rs7025262	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7029469	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7870848	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs912247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10817478	BSPRY	cis	parietal	SCAN
rs10817478	HDHD3	cis	Artery Tibial	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
3	chr9:116065400-116086800	Weak transcription	Gastric	stomach
4	chr9:116065600-116079000	Weak transcription	Fetal Intestine Small	intestine
5	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
6	chr9:116070000-116080000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:116070800-116083800	Weak transcription	Spleen	Spleen
8	chr9:116072000-116085200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:116072800-116079200	Weak transcription	Lung	lung
10	chr9:116072800-116080200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:116073000-116080400	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:116073200-116079600	Weak transcription	Fetal Lung	lung
13	chr9:116073200-116081000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:116073800-116080000	Weak transcription	Adipose Nuclei	Adipose
15	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:116074000-116079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:116074600-116079800	Weak transcription	Left Ventricle	heart
18	chr9:116074600-116080600	Weak transcription	Right Ventricle	heart
19	chr9:116075800-116079000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:116076000-116084600	Weak transcription	HSMMtube	muscle
21	chr9:116076200-116081000	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:116076200-116085000	Weak transcription	Placenta	Placenta
23	chr9:116076400-116078800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:116076400-116081000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:116076600-116078800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:116077000-116079000	Weak transcription	Fetal Intestine Large	intestine
27	chr9:116077000-116080600	Weak transcription	Fetal Kidney	kidney
28	chr9:116077000-116086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr9:116077200-116085600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:116077400-116079200	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:116077400-116080600	Weak transcription	Brain Angular Gyrus	brain
32	chr9:116077400-116080600	Weak transcription	Brain Substantia Nigra	brain
33	chr9:116077400-116082800	Weak transcription	Colonic Mucosa	Colon
34	chr9:116077400-116083800	Strong transcription	Ovary	ovary
35	chr9:116077400-116084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:116077400-116084200	Strong transcription	Fetal Stomach	stomach
37	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
38	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:116077600-116079400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:116077600-116079600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:116077600-116080400	Weak transcription	Fetal Brain Male	brain
42	chr9:116077800-116078800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:116077800-116079000	Weak transcription	Brain Anterior Caudate	brain
44	chr9:116077800-116082400	Weak transcription	Aorta	Aorta
45	chr9:116077800-116101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:116078000-116083800	Weak transcription	Primary T cells from cord blood	blood
47	chr9:116078400-116078600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:116078400-116078600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr9:116078400-116079600	Strong transcription	Pancreas	Pancrea
50	chr9:116078400-116084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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