Variant report

Variant	rs2761053
Chromosome Location	chr9:102879379-102879380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 167 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10116798	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10117150	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1014651	0.85[ASN][1000 genomes]
rs1014652	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10156395	0.81[ASN][1000 genomes]
rs10739795	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739796	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760710	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10760711	0.93[ASN][1000 genomes]
rs10760712	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10760720	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819714	0.93[ASN][1000 genomes]
rs10819715	0.93[ASN][1000 genomes]
rs10819716	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10819717	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10819719	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10819737	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819739	0.85[ASN][1000 genomes]
rs10988945	0.93[ASN][1000 genomes]
rs10988963	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10988968	0.94[ASN][1000 genomes]
rs10988969	0.94[ASN][1000 genomes]
rs10988973	0.96[ASN][1000 genomes]
rs10988974	0.96[ASN][1000 genomes]
rs10989009	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1099909	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12336751	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12552646	0.96[ASN][1000 genomes]
rs12685650	0.93[ASN][1000 genomes]
rs13301295	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1338119	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1342147	0.93[ASN][1000 genomes]
rs1361668	0.94[ASN][1000 genomes]
rs1406613	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1415926	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1418267	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1529191	0.93[ASN][1000 genomes]
rs1529192	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1529193	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1534726	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1535667	0.89[ASN][1000 genomes]
rs1539297	0.94[ASN][1000 genomes]
rs1572607	0.84[ASN][1000 genomes]
rs1578644	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1578645	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1578646	0.93[ASN][1000 genomes]
rs1852864	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1852865	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1891334	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1999877	0.85[ASN][1000 genomes]
rs2057476	0.96[ASN][1000 genomes]
rs2093696	0.93[ASN][1000 genomes]
rs2096158	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2104273	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181579	0.93[ASN][1000 genomes]
rs2209082	0.86[ASN][1000 genomes]
rs2416985	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2476439	0.85[ASN][1000 genomes]
rs2476441	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2476442	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2485746	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2491095	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2698999	0.88[ASN][1000 genomes]
rs2761056	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2787361	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787363	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2787364	0.87[ASN][1000 genomes]
rs2787365	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2787366	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2787391	0.86[AMR][1000 genomes]
rs2787393	0.80[ASN][1000 genomes]
rs2787394	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2787395	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2787397	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2791335	0.88[ASN][1000 genomes]
rs2791336	0.93[ASN][1000 genomes]
rs2791337	0.93[ASN][1000 genomes]
rs2795575	0.93[ASN][1000 genomes]
rs2806681	0.84[ASN][1000 genomes]
rs2806682	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2806683	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2806684	0.84[ASN][1000 genomes]
rs28448789	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35493819	0.81[ASN][1000 genomes]
rs3824510	0.81[ASN][1000 genomes]
rs41346545	0.93[ASN][1000 genomes]
rs4495492	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4503155	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4517187	0.94[ASN][1000 genomes]
rs4742779	0.93[ASN][1000 genomes]
rs4743375	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743376	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743378	0.81[ASN][1000 genomes]
rs4743379	0.89[ASN][1000 genomes]
rs4743380	0.89[ASN][1000 genomes]
rs4743381	0.86[ASN][1000 genomes]
rs4743382	0.93[ASN][1000 genomes]
rs4743384	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743386	0.96[ASN][1000 genomes]
rs6478991	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478994	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478995	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6478996	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478997	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478998	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6479000	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6479001	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479002	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7018981	0.94[ASN][1000 genomes]
rs7022493	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7024016	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7025300	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7026532	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027414	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7029020	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7029048	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7032333	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7033091	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7036518	0.89[ASN][1000 genomes]
rs7037362	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7041338	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7042194	0.93[ASN][1000 genomes]
rs7042912	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7043057	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7044219	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7045612	0.81[ASN][1000 genomes]
rs7047092	0.91[ASN][1000 genomes]
rs7846794	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847213	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853485	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7856844	0.85[ASN][1000 genomes]
rs7857530	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7858606	0.93[ASN][1000 genomes]
rs7859492	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7861003	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862460	0.93[ASN][1000 genomes]
rs7870585	0.91[ASN][1000 genomes]
rs7874449	0.89[ASN][1000 genomes]
rs846751	0.90[AMR][1000 genomes]
rs846752	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs846753	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs846754	0.96[ASN][1000 genomes]
rs846755	0.94[ASN][1000 genomes]
rs846756	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846758	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846759	0.96[ASN][1000 genomes]
rs846761	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846762	0.94[ASN][1000 genomes]
rs846765	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs846766	0.82[ASN][1000 genomes]
rs846768	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846769	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846770	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs860171	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs863668	0.85[ASN][1000 genomes]
rs9299337	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9408995	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409325	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs942163	0.93[ASN][1000 genomes]
rs9695692	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9886877	0.90[AMR][1000 genomes];0.89[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	nsv968739	chr9:102879081-102882884	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2761053	STX17	cis	Esophagus Mucosa	GTEx
rs2761053	STX17	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102862200-102879800	Weak transcription	Esophagus	oesophagus
2	chr9:102862200-102881000	Weak transcription	Gastric	stomach
3	chr9:102862200-102902400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:102862400-102881400	Weak transcription	Colonic Mucosa	Colon
5	chr9:102862800-102881800	Weak transcription	Right Ventricle	heart
6	chr9:102862800-102887400	Weak transcription	Pancreas	Pancrea
7	chr9:102867000-102881000	Weak transcription	Spleen	Spleen
8	chr9:102867000-102899800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:102868600-102895600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:102869000-102880200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:102869000-102881800	Weak transcription	Psoas Muscle	Psoas
12	chr9:102869000-102886600	Weak transcription	K562	blood
13	chr9:102869000-102888600	Weak transcription	Hela-S3	cervix
14	chr9:102869200-102889800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr9:102869200-102901800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:102869400-102899000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:102869800-102895600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:102869800-102896400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr9:102870000-102882800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:102870000-102887200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:102870000-102892200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:102870000-102895800	Weak transcription	Thymus	Thymus
23	chr9:102870000-102902200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:102870200-102881200	Weak transcription	Fetal Kidney	kidney
25	chr9:102870200-102891000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr9:102870600-102888600	Weak transcription	Fetal Thymus	thymus
27	chr9:102871000-102890200	Weak transcription	HUVEC	blood vessel
28	chr9:102871200-102890600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr9:102871200-102897400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:102871400-102890200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr9:102872000-102896600	Weak transcription	Placenta	Placenta
32	chr9:102872600-102883400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr9:102872800-102879400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:102872800-102895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:102873800-102882400	Weak transcription	Primary B cells from cord blood	blood
36	chr9:102873800-102888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:102873800-102895800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:102873800-102900200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr9:102874000-102884400	Weak transcription	GM12878-XiMat	blood
40	chr9:102874000-102888600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:102874000-102896000	Weak transcription	Colon Smooth Muscle	Colon
42	chr9:102874000-102896000	Weak transcription	Lung	lung
43	chr9:102874200-102879800	Weak transcription	HSMM	muscle
44	chr9:102874200-102880400	Weak transcription	NHLF	lung
45	chr9:102874200-102881800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:102874200-102882200	Weak transcription	Dnd41	blood
47	chr9:102874200-102882600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:102874200-102883200	Weak transcription	Liver	Liver
49	chr9:102874200-102884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:102874200-102884600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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