Variant report

Variant	rs814684
Chromosome Location	chr9:116721146-116721147
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116715151..116717735-chr9:116720132..116722087,2	MCF-7	breast:
2	chr9:116718450..116721380-chr9:116821221..116823441,2	MCF-7	breast:
3	chr9:116720397..116723417-chr9:116724656..116727366,3	MCF-7	breast:
4	chr9:116714888..116717726-chr9:116720128..116722306,2	K562	blood:
5	chr9:116716226..116718549-chr9:116720806..116723650,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11791817	1.00[GIH][hapmap]
rs11792006	1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs16910836	1.00[MEX][hapmap]
rs16910937	1.00[MEX][hapmap]
rs16910941	1.00[MEX][hapmap]
rs16910946	1.00[MEX][hapmap]
rs16910968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478053	1.00[MEX][hapmap]
rs7041279	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814678	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs814679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814681	0.91[EUR][1000 genomes]
rs814682	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814683	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814685	0.91[EUR][1000 genomes]
rs814687	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814691	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814694	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814695	0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers 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 miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs814684	BSPRY	cis	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116708800-116726400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:116710800-116723000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:116712800-116726400	Weak transcription	Brain Germinal Matrix	brain
4	chr9:116714400-116721200	Enhancers	NHDF-Ad	bronchial
5	chr9:116714600-116721600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:116714600-116722400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:116715000-116721200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:116716200-116730000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:116716800-116723000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:116717000-116721200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:116717000-116723400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:116717000-116730000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:116717000-116733200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:116717200-116754600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:116717400-116735600	Weak transcription	Fetal Heart	heart
16	chr9:116717600-116730200	Weak transcription	Psoas Muscle	Psoas
17	chr9:116717800-116724800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:116718000-116731400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:116718400-116728600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:116718600-116731000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:116719200-116721200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:116719200-116721200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:116719400-116721200	Enhancers	Lung	lung
24	chr9:116719400-116721200	Enhancers	Pancreas	Pancrea
25	chr9:116719600-116721200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:116719800-116721200	Enhancers	Fetal Intestine Large	intestine
27	chr9:116719800-116721200	Enhancers	Gastric	stomach
28	chr9:116719800-116721200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr9:116720000-116721200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:116720000-116722600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:116720000-116726000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:116720000-116726400	Weak transcription	Right Ventricle	heart
33	chr9:116720000-116728000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:116720000-116728000	Weak transcription	Spleen	Spleen
35	chr9:116720200-116721200	Enhancers	Placenta	Placenta
36	chr9:116720400-116721200	Enhancers	Left Ventricle	heart
37	chr9:116720400-116722400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:116720400-116731400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:116720400-116731400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:116720400-116731600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:116720400-116754200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr9:116720600-116721200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:116720600-116721200	Genic enhancers	HUVEC	blood vessel
44	chr9:116720600-116721200	Enhancers	NH-A	brain
45	chr9:116720600-116721200	Enhancers	NHEK	skin
46	chr9:116720600-116721200	Enhancers	NHLF	lung
47	chr9:116720600-116723400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr9:116720800-116721200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr9:116720800-116721200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:116720800-116721200	Enhancers	Fetal Kidney	kidney

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