Variant report

Variant	rs6759567
Chromosome Location	chr2:178301167-178301168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10172305	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10176724	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10180514	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10184488	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10190306	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10194452	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10497504	0.88[AFR][1000 genomes]
rs10497505	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10497506	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10497509	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10754987	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10754988	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10803911	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10803912	0.88[AFR][1000 genomes]
rs10930788	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10930789	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10930790	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10930791	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10930793	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10930796	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11891003	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12468046	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12478545	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12612957	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12621156	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12693121	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12990729	0.83[AFR][1000 genomes]
rs12997516	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13007779	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1345138	0.88[AFR][1000 genomes]
rs1348852	0.87[AMR][1000 genomes]
rs1349762	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1374438	0.90[AFR][1000 genomes]
rs1446837	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1446838	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1453369	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1530965	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1545363	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1584806	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17326999	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17398864	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1838890	0.88[AFR][1000 genomes]
rs1867905	0.88[AFR][1000 genomes]
rs1901823	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1979059	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2044493	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2084966	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2084967	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2100395	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2123643	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2141157	0.90[AFR][1000 genomes]
rs2166556	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2166557	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2167902	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2218575	0.88[AFR][1000 genomes]
rs2293475	0.88[AFR][1000 genomes]
rs2364846	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2364849	0.89[EUR][1000 genomes]
rs2364850	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2364851	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2364852	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2365616	0.87[AMR][1000 genomes]
rs3754989	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3813260	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3952496	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4144278	0.81[AFR][1000 genomes]
rs4243389	0.90[AFR][1000 genomes]
rs4308151	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4335983	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4350784	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4402804	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4585065	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4893822	0.85[AFR][1000 genomes]
rs4893824	0.85[AFR][1000 genomes]
rs4893825	0.80[AFR][1000 genomes]
rs4893826	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4893827	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4893829	0.88[AFR][1000 genomes]
rs4893933	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4893940	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4893942	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4893943	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4893951	0.85[AFR][1000 genomes]
rs4893955	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4893956	0.90[AFR][1000 genomes]
rs57890299	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6433664	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6433666	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6433674	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6433675	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6433676	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6433677	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6710109	0.90[AFR][1000 genomes]
rs6715365	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6717457	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6719114	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6720483	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6721168	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6723014	0.88[AFR][1000 genomes]
rs6725096	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6732250	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6739792	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6741974	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6744488	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6752779	0.87[AMR][1000 genomes]
rs6754660	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7568452	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7570297	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7582179	0.88[AFR][1000 genomes]
rs7585952	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7588049	0.88[AFR][1000 genomes]
rs7589927	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7594073	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7601132	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7604299	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7604668	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7607073	0.90[AFR][1000 genomes]
rs7608135	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9288001	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs935426	0.88[AFR][1000 genomes]
rs9789580	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9917193	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9917333	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[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
rs6759567	AGPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178287200-178310600	Weak transcription	Stomach Mucosa	stomach
2	chr2:178287600-178314200	Weak transcription	Gastric	stomach
3	chr2:178295400-178329800	Weak transcription	Pancreas	Pancrea
4	chr2:178295400-178330000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:178295400-178330200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:178295600-178306200	Weak transcription	Osteobl	bone
7	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:178296600-178319800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:178296800-178306800	Weak transcription	Placenta	Placenta
10	chr2:178296800-178310000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:178297000-178306000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:178297000-178313400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:178297200-178315400	Strong transcription	HepG2	liver
14	chr2:178297800-178301600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:178297800-178312800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:178297800-178314200	Weak transcription	Fetal Stomach	stomach
17	chr2:178297800-178319600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:178297800-178329800	Weak transcription	Ovary	ovary
19	chr2:178298000-178306400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:178298400-178301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:178298400-178306200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:178298400-178308800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:178298400-178309800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:178298400-178314200	Weak transcription	Left Ventricle	heart
25	chr2:178298600-178307200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:178298800-178301600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:178298800-178301600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:178298800-178302600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:178298800-178306800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:178298800-178309600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:178298800-178312600	Weak transcription	HSMMtube	muscle
32	chr2:178298800-178313600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:178298800-178313800	Strong transcription	Dnd41	blood
34	chr2:178298800-178314000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:178298800-178314000	Weak transcription	Fetal Intestine Small	intestine
36	chr2:178298800-178329200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:178298800-178329800	Weak transcription	Colonic Mucosa	Colon
38	chr2:178298800-178329800	Weak transcription	Thymus	Thymus
39	chr2:178298800-178330200	Weak transcription	Aorta	Aorta
40	chr2:178298800-178330200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:178298800-178331600	Weak transcription	NHDF-Ad	bronchial
42	chr2:178298800-178336800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:178298800-178357800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:178299000-178301200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:178299000-178301400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:178299000-178302800	Weak transcription	HUVEC	blood vessel
47	chr2:178299000-178303000	Weak transcription	Fetal Thymus	thymus
48	chr2:178299000-178304000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:178299000-178304200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:178299000-178306800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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