Variant report

Variant	rs10930790
Chromosome Location	chr2:178291873-178291874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10171135	0.84[CEU][hapmap]
rs10172305	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10176724	0.91[CEU][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10180514	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10184488	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190306	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10194452	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10208055	0.84[EUR][1000 genomes]
rs10497504	0.86[CEU][hapmap];0.91[AFR][1000 genomes]
rs10497505	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497506	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497509	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10754987	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10754988	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10803911	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10803912	0.84[CEU][hapmap];0.91[AFR][1000 genomes]
rs10930788	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10930789	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10930791	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930793	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10930796	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11891003	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12468046	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12478545	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12612957	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12621156	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12693121	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12990729	0.87[AFR][1000 genomes]
rs12997516	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13007779	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1345138	0.86[CEU][hapmap];0.91[AFR][1000 genomes]
rs1348852	0.91[CEU][hapmap]
rs1349762	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1374438	0.86[CEU][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1446837	0.91[CEU][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1446838	0.92[CEU][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1453369	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1530965	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1545363	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1584806	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17326999	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17398864	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1838890	0.91[AFR][1000 genomes]
rs1867905	0.86[CEU][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1901823	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1979059	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2044493	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2084966	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2084967	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2100395	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2123641	1.00[CEU][hapmap]
rs2123643	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2141157	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2166556	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2166557	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2167902	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167903	1.00[CEU][hapmap]
rs2178017	0.84[CEU][hapmap];0.82[AFR][1000 genomes]
rs2218575	0.86[CEU][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2293475	0.84[CEU][hapmap];0.91[AFR][1000 genomes]
rs2364846	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2364849	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2364850	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2364851	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364852	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2886194	1.00[CEU][hapmap]
rs3754989	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813260	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3952496	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4144278	0.86[CEU][hapmap];0.85[AFR][1000 genomes]
rs4243389	0.86[CEU][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4308151	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4335983	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350784	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4402804	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4585065	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4893822	0.89[AFR][1000 genomes]
rs4893824	0.89[AFR][1000 genomes]
rs4893825	0.84[AFR][1000 genomes]
rs4893826	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4893827	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4893829	0.84[CEU][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4893933	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4893940	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4893942	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4893943	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4893951	0.89[AFR][1000 genomes]
rs4893955	0.91[CEU][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4893956	0.86[CEU][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs57890299	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6433664	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433666	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433672	0.84[CEU][hapmap];0.82[AFR][1000 genomes]
rs6433674	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6433675	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433676	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433677	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6710109	0.86[CEU][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6715365	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6717457	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719114	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6720483	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6721168	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6723014	0.86[CEU][hapmap];0.91[AFR][1000 genomes]
rs6725096	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6725331	1.00[CEU][hapmap]
rs6732250	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737342	0.84[CEU][hapmap]
rs6739792	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6740092	1.00[CEU][hapmap]
rs6741974	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6744488	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6752528	0.84[CEU][hapmap]
rs6752779	0.92[CEU][hapmap]
rs6754660	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6759567	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7568452	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7570297	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582179	0.92[CEU][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7585952	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588049	0.84[CEU][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7589927	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7594073	0.91[CEU][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7601132	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604299	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7604668	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7607073	0.94[AFR][1000 genomes]
rs7608135	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9288001	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs935426	0.86[CEU][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9789580	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9917193	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9917333	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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
rs10930790	AGPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178258800-178294200	Weak transcription	Thymus	Thymus
2	chr2:178270400-178294400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:178272800-178295200	Weak transcription	Left Ventricle	heart
4	chr2:178276800-178294400	Weak transcription	Psoas Muscle	Psoas
5	chr2:178279600-178294400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:178280400-178296000	Weak transcription	Small Intestine	intestine
7	chr2:178280800-178294400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:178281200-178292200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:178283000-178294600	Weak transcription	Fetal Kidney	kidney
10	chr2:178283800-178294200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:178283800-178295200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:178284000-178294200	Weak transcription	NHLF	lung
13	chr2:178284400-178292000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:178284400-178292000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:178284400-178294000	Weak transcription	Fetal Thymus	thymus
16	chr2:178284600-178294000	Weak transcription	HSMM	muscle
17	chr2:178284600-178294400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:178284600-178295800	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:178284800-178294200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:178284800-178294400	Weak transcription	Liver	Liver
21	chr2:178285000-178294000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:178285600-178294200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:178285800-178294200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:178285800-178294400	Weak transcription	Placenta	Placenta
25	chr2:178285800-178294800	Weak transcription	Esophagus	oesophagus
26	chr2:178286200-178294200	Weak transcription	Aorta	Aorta
27	chr2:178287000-178294200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:178287000-178294200	Weak transcription	A549	lung
29	chr2:178287000-178296800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:178287200-178292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:178287200-178292400	Weak transcription	HepG2	liver
32	chr2:178287200-178295000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:178287200-178300000	Weak transcription	Hela-S3	cervix
34	chr2:178287200-178310600	Weak transcription	Stomach Mucosa	stomach
35	chr2:178287400-178292000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:178287400-178292200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:178287400-178294000	Weak transcription	NH-A	brain
38	chr2:178287600-178294200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:178287600-178294800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:178287600-178294800	Weak transcription	K562	blood
41	chr2:178287600-178314200	Weak transcription	Gastric	stomach
42	chr2:178288000-178297600	Weak transcription	HUVEC	blood vessel
43	chr2:178288200-178294400	Weak transcription	Spleen	Spleen
44	chr2:178288400-178292000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:178288800-178294000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:178289000-178294400	Weak transcription	Lung	lung
47	chr2:178289400-178299400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:178289600-178293000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:178291000-178299400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:178291600-178292000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood

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