Variant report

Variant	rs9789580
Chromosome Location	chr2:178329935-178329936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10172305	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10176724	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10180514	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10184488	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10190306	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10194452	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208055	0.84[EUR][1000 genomes]
rs10497504	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497505	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10497506	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10497509	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10754987	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10754988	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10803911	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10803912	0.94[AFR][1000 genomes]
rs10930788	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10930789	0.95[EUR][1000 genomes]
rs10930790	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10930791	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10930793	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10930796	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11891003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468046	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478545	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12612957	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621156	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12693121	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990729	0.84[AFR][1000 genomes]
rs12997516	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007779	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345138	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348852	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1349762	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1374438	0.96[AFR][1000 genomes]
rs1446837	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1446838	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1453369	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1530965	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1545363	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584806	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17326999	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17398864	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838890	0.94[AFR][1000 genomes]
rs1867905	0.94[AFR][1000 genomes]
rs1901823	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1979059	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044493	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084966	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2084967	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2100395	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2123643	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2141157	0.96[AFR][1000 genomes]
rs2166556	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166557	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2167902	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2178017	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218575	0.94[AFR][1000 genomes]
rs2293475	0.94[AFR][1000 genomes]
rs2364846	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2364849	0.95[EUR][1000 genomes]
rs2364850	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2364851	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2364852	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2365616	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3754989	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3813260	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3952496	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4144278	0.87[AFR][1000 genomes]
rs4243389	0.96[AFR][1000 genomes]
rs4308151	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4335983	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4350784	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4402804	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4585065	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4893822	0.86[AFR][1000 genomes]
rs4893824	0.86[AFR][1000 genomes]
rs4893825	0.81[AFR][1000 genomes]
rs4893826	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4893827	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4893829	0.94[AFR][1000 genomes]
rs4893933	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4893940	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4893942	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4893943	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4893951	0.86[AFR][1000 genomes]
rs4893955	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4893956	0.96[AFR][1000 genomes]
rs57890299	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6433664	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433666	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6433672	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433674	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6433675	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433676	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433677	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6710109	0.96[AFR][1000 genomes]
rs6715365	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717457	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6719114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720483	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6721168	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6723014	0.94[AFR][1000 genomes]
rs6725096	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6732250	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6739792	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6741974	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6744488	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6752779	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6754660	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6759567	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7568452	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7570297	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7582179	0.94[AFR][1000 genomes]
rs7585952	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7588049	0.94[AFR][1000 genomes]
rs7589927	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594073	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7601132	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604299	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7604668	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7607073	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608135	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288001	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs935426	0.94[AFR][1000 genomes]
rs9917193	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9917333	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9789580	AGPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178295400-178330000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:178295400-178330200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:178298800-178330200	Weak transcription	Aorta	Aorta
5	chr2:178298800-178330200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:178298800-178331600	Weak transcription	NHDF-Ad	bronchial
7	chr2:178298800-178336800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:178298800-178357800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:178299000-178330200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:178299400-178357800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:178300800-178331400	Weak transcription	Psoas Muscle	Psoas
12	chr2:178301000-178330200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:178301600-178339800	Weak transcription	Small Intestine	intestine
14	chr2:178301800-178339200	Weak transcription	Hela-S3	cervix
15	chr2:178304400-178338800	Weak transcription	HMEC	breast
16	chr2:178305600-178330000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:178305800-178330200	Weak transcription	Brain Substantia Nigra	brain
18	chr2:178306000-178331200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:178306600-178330400	Weak transcription	Brain Angular Gyrus	brain
20	chr2:178307200-178330200	Weak transcription	NHEK	skin
21	chr2:178307800-178330600	Weak transcription	Osteobl	bone
22	chr2:178310800-178330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:178311200-178330200	Weak transcription	Lung	lung
24	chr2:178313000-178330400	Weak transcription	Right Atrium	heart
25	chr2:178313400-178330200	Weak transcription	HSMMtube	muscle
26	chr2:178313800-178331400	Weak transcription	NH-A	brain
27	chr2:178314000-178331600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:178314200-178330200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:178314400-178330000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:178314400-178330000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:178314400-178330200	Weak transcription	Gastric	stomach
32	chr2:178314400-178330200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:178314400-178330200	Weak transcription	Spleen	Spleen
34	chr2:178314400-178330400	Weak transcription	Fetal Brain Female	brain
35	chr2:178314400-178330600	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:178314400-178331600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:178314600-178330000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:178314600-178330000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:178315600-178330200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:178316000-178333200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:178316200-178345600	Weak transcription	Fetal Brain Male	brain
42	chr2:178317600-178330200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:178320000-178336200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:178320200-178330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:178321000-178330000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:178321000-178330200	Weak transcription	Left Ventricle	heart
47	chr2:178321400-178330200	Weak transcription	GM12878-XiMat	blood
48	chr2:178321600-178331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:178325000-178335800	Strong transcription	HepG2	liver
50	chr2:178325200-178330000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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