Variant report

Variant	rs10989009
Chromosome Location	chr9:102957990-102957991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 195 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:189)

rs_ID	r²[population]
rs10116798	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014651	0.93[ASN][1000 genomes]
rs1014652	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10156395	0.81[ASN][1000 genomes]
rs10739795	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10739796	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760710	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10760711	0.89[ASN][1000 genomes]
rs10760712	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10760720	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819714	0.89[ASN][1000 genomes]
rs10819715	0.89[ASN][1000 genomes]
rs10819716	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10819717	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10819719	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10819737	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819739	0.96[ASN][1000 genomes]
rs10819751	0.85[AMR][1000 genomes]
rs10988945	0.89[ASN][1000 genomes]
rs10988963	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10988968	0.87[ASN][1000 genomes]
rs10988969	0.87[ASN][1000 genomes]
rs10988973	0.86[ASN][1000 genomes]
rs10988974	0.86[ASN][1000 genomes]
rs1099909	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1099910	0.89[ASN][1000 genomes]
rs12336751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552646	0.86[ASN][1000 genomes]
rs12685650	0.89[ASN][1000 genomes]
rs13301295	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1338119	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1338123	0.83[EUR][1000 genomes]
rs1338124	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1338125	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1342147	0.89[ASN][1000 genomes]
rs1361668	0.87[ASN][1000 genomes]
rs1406613	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1415926	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418267	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1529191	0.89[ASN][1000 genomes]
rs1529192	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1529193	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1534726	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1535667	0.93[ASN][1000 genomes]
rs1539297	0.87[ASN][1000 genomes]
rs1572607	0.94[ASN][1000 genomes]
rs1578644	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1578645	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1578646	0.89[ASN][1000 genomes]
rs1852864	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1852865	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1891334	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1999877	0.93[ASN][1000 genomes]
rs2057476	0.86[ASN][1000 genomes]
rs2093696	0.89[ASN][1000 genomes]
rs2096158	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2104273	0.89[ASN][1000 genomes]
rs2181579	0.86[ASN][1000 genomes]
rs2209082	0.83[ASN][1000 genomes]
rs2245216	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2476439	0.96[ASN][1000 genomes]
rs2476441	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476442	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485745	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2485746	0.90[AMR][1000 genomes]
rs2491095	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2491096	0.89[ASN][1000 genomes]
rs2698999	0.84[ASN][1000 genomes]
rs2761053	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2761056	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787361	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2787363	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2787364	0.91[ASN][1000 genomes]
rs2787365	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787366	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787368	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2787369	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2787371	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2787372	0.82[EUR][1000 genomes]
rs2787373	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2787377	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2787380	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2787381	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2787383	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2787385	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2787388	0.84[EUR][1000 genomes]
rs2787391	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2787393	0.87[ASN][1000 genomes]
rs2787394	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2787395	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2787396	0.87[ASN][1000 genomes]
rs2787397	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2791335	0.84[ASN][1000 genomes]
rs2791336	0.89[ASN][1000 genomes]
rs2791337	0.89[ASN][1000 genomes]
rs2795575	0.89[ASN][1000 genomes]
rs2806681	0.91[ASN][1000 genomes]
rs2806682	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2806683	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806684	0.91[ASN][1000 genomes]
rs2806685	0.87[ASN][1000 genomes]
rs2806687	0.87[ASN][1000 genomes]
rs2806688	0.89[ASN][1000 genomes]
rs2806692	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2806693	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2806694	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2806695	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2806696	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28448789	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3813712	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3824510	0.81[ASN][1000 genomes]
rs41346545	0.89[ASN][1000 genomes]
rs4495492	0.86[ASN][1000 genomes]
rs4503155	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4517187	0.87[ASN][1000 genomes]
rs4742779	0.89[ASN][1000 genomes]
rs4743375	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4743376	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4743378	0.81[ASN][1000 genomes]
rs4743379	0.85[ASN][1000 genomes]
rs4743380	0.85[ASN][1000 genomes]
rs4743381	0.83[ASN][1000 genomes]
rs4743382	0.89[ASN][1000 genomes]
rs4743384	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4743386	0.86[ASN][1000 genomes]
rs6478991	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6478994	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6478995	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6478996	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6478997	0.89[ASN][1000 genomes]
rs6478998	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6479000	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6479001	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6479002	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7018981	0.87[ASN][1000 genomes]
rs7022493	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7024016	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7025300	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7026532	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7027414	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7029020	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7029048	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7032333	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7033091	0.89[ASN][1000 genomes]
rs7036518	0.86[ASN][1000 genomes]
rs7037362	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7041338	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7042194	0.89[ASN][1000 genomes]
rs7042912	0.89[ASN][1000 genomes]
rs7043057	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7044219	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7045612	0.81[ASN][1000 genomes]
rs7047092	0.88[ASN][1000 genomes]
rs7846794	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7847213	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7853485	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7856844	0.96[ASN][1000 genomes]
rs7857530	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7858606	0.89[ASN][1000 genomes]
rs7859492	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7861003	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7862460	0.89[ASN][1000 genomes]
rs7870585	0.88[ASN][1000 genomes]
rs7874449	0.86[ASN][1000 genomes]
rs846751	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs846752	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846753	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs846754	0.86[ASN][1000 genomes]
rs846755	0.87[ASN][1000 genomes]
rs846756	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846758	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846759	0.86[ASN][1000 genomes]
rs846761	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846762	0.87[ASN][1000 genomes]
rs846763	0.89[ASN][1000 genomes]
rs846765	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846766	0.92[ASN][1000 genomes]
rs846768	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846769	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846770	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860171	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs863668	0.96[ASN][1000 genomes]
rs9299337	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9408995	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9409325	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs942163	0.89[ASN][1000 genomes]
rs9695692	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886877	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	esv3366028	chr9:102947446-102973079	Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10989009	STX17	cis	Esophagus Mucosa	GTEx
rs10989009	STX17	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102940200-102959200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:102940400-102959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:102940400-102978000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:102952400-102963400	Weak transcription	Pancreas	Pancrea
5	chr9:102953000-102976800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:102953800-102977600	Weak transcription	Fetal Stomach	stomach
7	chr9:102954000-102959200	Weak transcription	Liver	Liver
8	chr9:102954600-102958400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:102954600-102960400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:102954600-102963600	Weak transcription	Fetal Heart	heart
11	chr9:102954600-102966600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:102954600-102967400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:102954600-102972200	Weak transcription	Primary B cells from cord blood	blood
14	chr9:102954600-102978000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:102954800-102960400	Weak transcription	Esophagus	oesophagus
16	chr9:102954800-102961800	Weak transcription	Primary T cells from cord blood	blood
17	chr9:102954800-102963200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:102954800-102967400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:102954800-102968600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:102954800-102972000	Weak transcription	Left Ventricle	heart
21	chr9:102955000-102988400	Weak transcription	Dnd41	blood
22	chr9:102955200-102959200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:102955200-102999600	Weak transcription	Lung	lung
24	chr9:102955400-102962400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr9:102955600-102959800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:102955600-102960800	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:102955600-102961000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:102955800-102958200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:102956000-102958400	Weak transcription	Fetal Intestine Large	intestine
30	chr9:102956000-102959800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr9:102956000-102972000	Weak transcription	GM12878-XiMat	blood
32	chr9:102956200-102958600	Weak transcription	Fetal Intestine Small	intestine
33	chr9:102956200-102983400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:102956400-102961200	Weak transcription	Adipose Nuclei	Adipose
35	chr9:102956400-102961400	Weak transcription	Fetal Lung	lung
36	chr9:102956400-102961600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr9:102956600-102958400	Weak transcription	HepG2	liver
38	chr9:102956600-102961000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:102956600-102961400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:102956800-102959200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:102957200-102973200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:102957400-102959000	Weak transcription	Ovary	ovary
43	chr9:102957400-102977800	Weak transcription	Aorta	Aorta

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