Variant report

Variant	rs10114327
Chromosome Location	chr9:116093790-116093791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116091449..116094429-chr9:116104938..116107109,2	MCF-7	breast:
2	chr9:116091769..116094261-chr9:116096086..116099687,3	MCF-7	breast:
3	chr9:116093601..116095612-chr9:116137576..116139451,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119431	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10117906	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118045	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118275	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10759640	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759641	0.95[EUR][1000 genomes]
rs10817481	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817485	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10981762	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10981763	0.88[ASN][1000 genomes]
rs11787602	0.89[ASN][1000 genomes]
rs1323466	0.94[AFR][1000 genomes]
rs1998504	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2093691	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296073	0.85[AFR][1000 genomes]
rs3810921	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6478002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478003	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478004	0.88[ASN][1000 genomes]
rs6478005	0.88[ASN][1000 genomes]
rs6478006	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025188	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025371	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7025517	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025770	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7026076	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7027833	0.86[AFR][1000 genomes]
rs7041572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7048039	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849513	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850002	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850264	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7863921	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7864788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868271	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10114327	BSPRY	cis	Heart Left Ventricle	GTEx
rs10114327	PRPF4	cis	Esophagus Muscularis	GTEx
rs10114327	CDC26	cis	Esophagus Muscularis	GTEx
rs10114327	CDC26	cis	Muscle Skeletal	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	chr9:116079000-116094600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:116080800-116101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:116080800-116101600	Weak transcription	Fetal Brain Male	brain
8	chr9:116081000-116101600	Weak transcription	Pancreas	Pancrea
9	chr9:116081400-116098000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:116082200-116101600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:116082600-116101400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:116082800-116101400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:116082800-116101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:116082800-116101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:116082800-116101600	Weak transcription	Brain Substantia Nigra	brain
16	chr9:116082800-116101600	Weak transcription	Fetal Kidney	kidney
17	chr9:116082800-116101600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:116082800-116102000	Weak transcription	Aorta	Aorta
19	chr9:116083000-116101400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr9:116083800-116094000	Weak transcription	Left Ventricle	heart
21	chr9:116083800-116101200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:116083800-116101200	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:116083800-116101400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:116083800-116101600	Weak transcription	Right Ventricle	heart
25	chr9:116084000-116101400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:116084200-116101200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:116084200-116101400	Weak transcription	Liver	Liver
28	chr9:116084200-116101400	Weak transcription	Brain Anterior Caudate	brain
29	chr9:116084200-116101400	Weak transcription	Fetal Stomach	stomach
30	chr9:116084200-116101600	Weak transcription	Fetal Muscle Leg	muscle
31	chr9:116085400-116101400	Weak transcription	Adipose Nuclei	Adipose
32	chr9:116085400-116101400	Weak transcription	Fetal Lung	lung
33	chr9:116085400-116101600	Weak transcription	Brain Angular Gyrus	brain
34	chr9:116085600-116101200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:116091400-116101400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:116092000-116101400	Weak transcription	Small Intestine	intestine
37	chr9:116093000-116101400	Weak transcription	Fetal Intestine Small	intestine
38	chr9:116093000-116101800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr9:116093600-116093800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:116093600-116094400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:116093600-116094400	Strong transcription	Ovary	ovary
42	chr9:116093600-116101200	Weak transcription	Stomach Smooth Muscle	stomach

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