Variant report

Variant	rs7041572
Chromosome Location	chr9:116085602-116085603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116084742..116086988-chr9:116101067..116102910,3	MCF-7	breast:
2	chr9:116079992..116082987-chr9:116085261..116087618,2	K562	blood:
3	chr9:116079992..116082987-chr9:116084415..116087618,3	K562	blood:

Variant related genes	Relation type
ENSG00000148225	Chromatin interaction

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

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

rs_ID	r²[population]
rs10114327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10117906	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10118045	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10118275	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10759640	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759641	0.95[EUR][1000 genomes]
rs10817481	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817485	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10981762	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10981763	0.86[ASN][1000 genomes]
rs11787602	0.87[ASN][1000 genomes]
rs1323466	0.96[AFR][1000 genomes]
rs1998504	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2093691	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296073	0.87[AFR][1000 genomes]
rs3810921	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6478002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478003	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478004	0.87[ASN][1000 genomes]
rs6478005	0.87[ASN][1000 genomes]
rs6478006	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7025188	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7025371	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025517	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7025770	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7026076	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7027833	0.88[AFR][1000 genomes]
rs7048039	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7849513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850002	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7850264	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7863921	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7864788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868271	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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
rs7041572	CDC26	cis	Esophagus Muscularis	GTEx
rs7041572	BSPRY	cis	Heart Left Ventricle	GTEx
rs7041572	CDC26	cis	Muscle Skeletal	GTEx
rs7041572	PRPF4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
2	chr9:116065400-116086800	Weak transcription	Gastric	stomach
3	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:116077000-116086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:116077800-116101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:116078400-116086400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr9:116078800-116093600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:116079000-116094600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:116079600-116086000	Weak transcription	Fetal Brain Female	brain
12	chr9:116079800-116087600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:116080600-116086600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:116080800-116101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:116080800-116101600	Weak transcription	Fetal Brain Male	brain
16	chr9:116081000-116101600	Weak transcription	Pancreas	Pancrea
17	chr9:116081400-116098000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:116082200-116101600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:116082600-116101400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:116082800-116101400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:116082800-116101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:116082800-116101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:116082800-116101600	Weak transcription	Brain Substantia Nigra	brain
24	chr9:116082800-116101600	Weak transcription	Fetal Kidney	kidney
25	chr9:116082800-116101600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:116082800-116102000	Weak transcription	Aorta	Aorta
27	chr9:116083000-116101400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:116083800-116087200	Weak transcription	Lung	lung
29	chr9:116083800-116090400	Weak transcription	Fetal Intestine Small	intestine
30	chr9:116083800-116093600	Weak transcription	Ovary	ovary
31	chr9:116083800-116094000	Weak transcription	Left Ventricle	heart
32	chr9:116083800-116101200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:116083800-116101200	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:116083800-116101400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:116083800-116101600	Weak transcription	Right Ventricle	heart
36	chr9:116084000-116093600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:116084000-116101400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:116084200-116087000	Weak transcription	Esophagus	oesophagus
39	chr9:116084200-116101200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:116084200-116101400	Weak transcription	Liver	Liver
41	chr9:116084200-116101400	Weak transcription	Brain Anterior Caudate	brain
42	chr9:116084200-116101400	Weak transcription	Fetal Stomach	stomach
43	chr9:116084200-116101600	Weak transcription	Fetal Muscle Leg	muscle
44	chr9:116085400-116092000	Weak transcription	HSMMtube	muscle
45	chr9:116085400-116101400	Weak transcription	Adipose Nuclei	Adipose
46	chr9:116085400-116101400	Weak transcription	Fetal Lung	lung
47	chr9:116085400-116101600	Weak transcription	Brain Angular Gyrus	brain
48	chr9:116085600-116101200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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