Variant report

Variant	rs987553
Chromosome Location	chr9:95298694-95298695
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr9:95298656-95299073	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:95298417-95298788	K562	blood:	n/a	n/a
3	GATA3	chr9:95298383-95298852	SK-N-SH	brain:	n/a	chr9:95298643-95298650 chr9:95298638-95298650
4	CEBPB	chr9:95298424-95298910	IMR90	lung:	n/a	n/a
5	STAT3	chr9:95298629-95298942	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr9:95298270-95298982	SK-N-SH	brain:	n/a	chr9:95298643-95298650 chr9:95298638-95298650

Variant related genes	Relation type
ECM2	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10114912	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10114932	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10115290	0.81[EUR][1000 genomes]
rs10116813	0.81[EUR][1000 genomes]
rs10117627	0.81[EUR][1000 genomes]
rs10117680	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10118107	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10118939	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10124058	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10125450	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10125587	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10429459	0.84[EUR][1000 genomes]
rs10514815	0.86[EUR][1000 genomes]
rs1075397	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10761155	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10761158	0.81[EUR][1000 genomes]
rs10761160	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10761163	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761164	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10820968	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10820980	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10820989	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10820994	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10821008	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992304	0.81[EUR][1000 genomes]
rs10992347	0.82[EUR][1000 genomes]
rs10992349	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992365	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992366	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992393	0.80[EUR][1000 genomes]
rs10992457	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1121978	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11788511	0.96[ASN][1000 genomes]
rs11788523	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11791001	0.89[ASN][1000 genomes]
rs11791339	0.96[ASN][1000 genomes]
rs11791805	0.96[ASN][1000 genomes]
rs11792019	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11792916	0.89[ASN][1000 genomes]
rs11793727	0.94[ASN][1000 genomes]
rs11794346	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12335553	0.85[AFR][1000 genomes]
rs12336415	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12336884	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12338938	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12341817	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12342019	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12343820	0.83[EUR][1000 genomes]
rs13286566	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13301492	0.80[EUR][1000 genomes]
rs13301537	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13301652	0.83[EUR][1000 genomes]
rs1380	0.89[ASN][1000 genomes]
rs1535754	0.81[EUR][1000 genomes]
rs1535756	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1924243	0.81[EUR][1000 genomes]
rs1924244	0.83[EUR][1000 genomes]
rs1980848	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2026585	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2094281	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2104533	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2296666	0.89[EUR][1000 genomes]
rs2296669	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2516568	0.84[AMR][1000 genomes]
rs2761677	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2761678	0.91[ASN][1000 genomes]
rs2761681	0.84[AMR][1000 genomes]
rs2895219	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3739606	0.83[EUR][1000 genomes]
rs3780347	0.85[EUR][1000 genomes]
rs3927488	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743873	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4743874	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743875	0.80[EUR][1000 genomes]
rs4744133	0.82[EUR][1000 genomes]
rs4744135	0.86[EUR][1000 genomes]
rs4744137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744139	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4744141	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62572543	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6479422	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6479423	0.85[EUR][1000 genomes]
rs7029879	0.89[ASN][1000 genomes]
rs7029939	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7030920	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7031567	0.84[EUR][1000 genomes]
rs7033979	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7043984	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7045572	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs724102	0.82[EUR][1000 genomes]
rs747628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs747629	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7847534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7848472	0.94[ASN][1000 genomes]
rs7849788	0.82[EUR][1000 genomes]
rs7849927	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7850528	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7852698	0.82[EUR][1000 genomes]
rs7860786	0.86[EUR][1000 genomes]
rs7863049	0.82[EUR][1000 genomes]
rs7864575	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7865019	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7868013	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7869521	0.80[EUR][1000 genomes]
rs7872610	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872644	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7873390	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7873397	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7874151	0.94[ASN][1000 genomes]
rs927865	0.86[EUR][1000 genomes]
rs9299405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs968040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs987554	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs987553	CENPP	cis	Esophagus Muscularis	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95269800-95298800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:95294800-95301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:95296000-95301800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:95296400-95299600	Enhancers	HepG2	liver
5	chr9:95296600-95298800	Active TSS	Stomach Smooth Muscle	stomach
6	chr9:95296600-95299000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr9:95296800-95298800	Active TSS	Rectal Smooth Muscle	rectum
8	chr9:95297000-95299200	Active TSS	Right Atrium	heart
9	chr9:95297200-95301000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:95297400-95298800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:95297400-95298800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:95297400-95298800	Active TSS	Fetal Muscle Leg	muscle
13	chr9:95297400-95298800	Active TSS	NHLF	lung
14	chr9:95297400-95299000	Active TSS	Adipose Nuclei	Adipose
15	chr9:95297400-95299200	Active TSS	Fetal Lung	lung
16	chr9:95297400-95299200	Active TSS	Ovary	ovary
17	chr9:95297400-95299400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:95297400-95300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:95297400-95300000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:95297400-95304600	Weak transcription	Left Ventricle	heart
21	chr9:95297600-95299200	Active TSS	NHDF-Ad	bronchial
22	chr9:95297800-95299200	Active TSS	Liver	Liver
23	chr9:95298000-95299000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr9:95298000-95299000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:95298000-95299000	Active TSS	Duodenum Mucosa	Duodenum
26	chr9:95298000-95299000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr9:95298000-95299000	Active TSS	Fetal Intestine Large	intestine
28	chr9:95298000-95299200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:95298000-95299600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr9:95298200-95298800	Active TSS	Fetal Intestine Small	intestine
31	chr9:95298200-95298800	Active TSS	HSMM	muscle
32	chr9:95298200-95299000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:95298200-95299000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:95298200-95299000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr9:95298200-95299000	Active TSS	Aorta	Aorta
36	chr9:95298200-95299000	Active TSS	Brain Anterior Caudate	brain
37	chr9:95298200-95299200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr9:95298400-95298800	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr9:95298400-95298800	Active TSS	HSMMtube	muscle
40	chr9:95298400-95299000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr9:95298400-95299000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr9:95298400-95299000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:95298400-95299000	Active TSS	Brain Cingulate Gyrus	brain
44	chr9:95298400-95299000	Active TSS	Colon Smooth Muscle	Colon
45	chr9:95298400-95299000	Flanking Active TSS	Fetal Kidney	kidney
46	chr9:95298400-95299000	Enhancers	Fetal Stomach	stomach
47	chr9:95298400-95299000	Active TSS	Psoas Muscle	Psoas
48	chr9:95298400-95299000	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr9:95298400-95299000	Enhancers	Stomach Mucosa	stomach
50	chr9:95298400-95299000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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