Variant report

Variant	rs2296076
Chromosome Location	chr9:116079271-116079272
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116079156..116083300-chr9:116100482..116103976,4	MCF-7	breast:
2	chr9:116077143..116079692-chr9:116110149..116111989,2	MCF-7	breast:
3	chr9:116037629..116039363-chr9:116078698..116081289,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136875	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000148225	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10817477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981711	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10981713	1.00[CEU][hapmap]
rs10981714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981718	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981719	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981721	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981725	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981734	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10981736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981754	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12350131	0.84[ASN][1000 genomes]
rs12684385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12982	0.82[CEU][hapmap]
rs13289574	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16926630	0.82[CEU][hapmap]
rs16930959	1.00[CEU][hapmap]
rs16932083	0.94[EUR][1000 genomes]
rs16932730	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16932806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296074	1.00[ASW][hapmap]
rs2296075	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2418249	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs28480972	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34289746	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34294772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34429100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34749539	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35275471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35772163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35852964	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35860025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35915957	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810915	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs3810920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4641140	1.00[CEU][hapmap]
rs59841233	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61161242	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71503561	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7850003	0.96[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
rs2296076	WDR31	cis	lymphoblastoid	seeQTL
rs2296076	WDR31	cis	Esophagus Mucosa	GTEx

Chromatin state (count:54 , 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	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
5	chr9:116070000-116080000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:116070800-116083800	Weak transcription	Spleen	Spleen
7	chr9:116072000-116085200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:116072800-116080200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:116073000-116080400	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:116073200-116079600	Weak transcription	Fetal Lung	lung
11	chr9:116073200-116081000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:116073800-116080000	Weak transcription	Adipose Nuclei	Adipose
13	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:116074000-116079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:116074600-116079800	Weak transcription	Left Ventricle	heart
16	chr9:116074600-116080600	Weak transcription	Right Ventricle	heart
17	chr9:116076000-116084600	Weak transcription	HSMMtube	muscle
18	chr9:116076200-116081000	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:116076200-116085000	Weak transcription	Placenta	Placenta
20	chr9:116076400-116081000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:116077000-116080600	Weak transcription	Fetal Kidney	kidney
22	chr9:116077000-116086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:116077200-116085600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:116077400-116080600	Weak transcription	Brain Angular Gyrus	brain
25	chr9:116077400-116080600	Weak transcription	Brain Substantia Nigra	brain
26	chr9:116077400-116082800	Weak transcription	Colonic Mucosa	Colon
27	chr9:116077400-116083800	Strong transcription	Ovary	ovary
28	chr9:116077400-116084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:116077400-116084200	Strong transcription	Fetal Stomach	stomach
30	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
31	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:116077600-116079400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:116077600-116079600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:116077600-116080400	Weak transcription	Fetal Brain Male	brain
35	chr9:116077800-116082400	Weak transcription	Aorta	Aorta
36	chr9:116077800-116101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:116078000-116083800	Weak transcription	Primary T cells from cord blood	blood
38	chr9:116078400-116079600	Strong transcription	Pancreas	Pancrea
39	chr9:116078400-116084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:116078400-116086400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr9:116078600-116080600	Weak transcription	Liver	Liver
42	chr9:116078600-116082600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:116078600-116083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:116078800-116082200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr9:116078800-116082800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:116078800-116093600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr9:116079000-116080000	Strong transcription	Fetal Intestine Small	intestine
48	chr9:116079000-116080800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:116079000-116081800	Strong transcription	Fetal Intestine Large	intestine
50	chr9:116079000-116083800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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