Variant report

Variant	rs6741974
Chromosome Location	chr2:178295573-178295574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 191 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10172305	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173008	1.00[ASN][1000 genomes]
rs10173172	1.00[ASN][1000 genomes]
rs10176724	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179735	1.00[ASN][1000 genomes]
rs10180514	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10184488	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10190306	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10194452	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10196753	1.00[ASN][1000 genomes]
rs10196915	1.00[ASN][1000 genomes]
rs10208055	0.85[EUR][1000 genomes]
rs10497504	0.91[AFR][1000 genomes]
rs10497505	0.91[EUR][1000 genomes]
rs10497506	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10497509	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10497510	1.00[ASN][1000 genomes]
rs10754987	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10754988	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10803911	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10803912	0.91[AFR][1000 genomes]
rs10930786	1.00[ASN][1000 genomes]
rs10930788	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10930789	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930790	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10930791	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10930793	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10930796	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11889478	1.00[ASN][1000 genomes]
rs11891003	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12468046	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12478545	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12612957	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12621156	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693118	1.00[ASN][1000 genomes]
rs12693119	1.00[ASN][1000 genomes]
rs12693121	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12990729	0.87[AFR][1000 genomes]
rs12997516	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13007779	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1345138	0.91[AFR][1000 genomes]
rs1348852	0.84[AMR][1000 genomes]
rs1349762	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374438	0.94[AFR][1000 genomes]
rs1377491	1.00[ASN][1000 genomes]
rs1446837	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1446838	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1453369	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453376	1.00[ASN][1000 genomes]
rs1463287	1.00[ASN][1000 genomes]
rs1463288	1.00[ASN][1000 genomes]
rs1466208	1.00[ASN][1000 genomes]
rs1530965	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1545363	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1551287	1.00[ASN][1000 genomes]
rs1551288	1.00[ASN][1000 genomes]
rs1551289	1.00[ASN][1000 genomes]
rs1551290	1.00[ASN][1000 genomes]
rs1584806	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597959	1.00[ASN][1000 genomes]
rs17326999	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17398864	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17648502	1.00[ASN][1000 genomes]
rs1838890	0.91[AFR][1000 genomes]
rs1867905	0.91[AFR][1000 genomes]
rs1869357	1.00[ASN][1000 genomes]
rs1901823	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1901828	1.00[ASN][1000 genomes]
rs1973045	1.00[ASN][1000 genomes]
rs1979059	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2044493	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2084966	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084967	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2100395	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2123641	1.00[ASN][1000 genomes]
rs2123643	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123644	1.00[ASN][1000 genomes]
rs2123645	1.00[ASN][1000 genomes]
rs2141157	0.94[AFR][1000 genomes]
rs2166556	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2166557	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2167902	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2167903	1.00[ASN][1000 genomes]
rs2167904	1.00[ASN][1000 genomes]
rs2178017	0.82[AFR][1000 genomes]
rs2218575	0.91[AFR][1000 genomes]
rs2293475	0.91[AFR][1000 genomes]
rs2364846	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364847	1.00[ASN][1000 genomes]
rs2364849	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364850	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364851	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2364852	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2365616	0.84[AMR][1000 genomes]
rs2444563	1.00[ASN][1000 genomes]
rs2444564	1.00[ASN][1000 genomes]
rs2464655	1.00[ASN][1000 genomes]
rs2602527	1.00[ASN][1000 genomes]
rs2602528	1.00[ASN][1000 genomes]
rs2706143	1.00[ASN][1000 genomes]
rs2706144	1.00[ASN][1000 genomes]
rs2706145	1.00[ASN][1000 genomes]
rs2706146	1.00[ASN][1000 genomes]
rs2706150	1.00[ASN][1000 genomes]
rs2706153	1.00[ASN][1000 genomes]
rs2706154	1.00[ASN][1000 genomes]
rs2706155	1.00[ASN][1000 genomes]
rs2706156	1.00[ASN][1000 genomes]
rs2706157	1.00[ASN][1000 genomes]
rs2706158	1.00[ASN][1000 genomes]
rs2706162	1.00[ASN][1000 genomes]
rs2706163	1.00[ASN][1000 genomes]
rs3754989	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3813260	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3952496	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144278	0.85[AFR][1000 genomes]
rs4243389	0.94[AFR][1000 genomes]
rs4308151	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4335983	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4350784	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402804	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4585065	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4893822	0.89[AFR][1000 genomes]
rs4893824	0.89[AFR][1000 genomes]
rs4893825	0.84[AFR][1000 genomes]
rs4893826	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893827	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893829	0.91[AFR][1000 genomes]
rs4893933	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893940	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4893942	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4893943	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4893951	0.89[AFR][1000 genomes]
rs4893955	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4893956	0.94[AFR][1000 genomes]
rs56951837	1.00[ASN][1000 genomes]
rs57890299	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6433661	1.00[ASN][1000 genomes]
rs6433662	1.00[ASN][1000 genomes]
rs6433664	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6433666	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6433672	0.82[AFR][1000 genomes]
rs6433674	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433675	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6433676	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6433677	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6710109	0.94[AFR][1000 genomes]
rs6715365	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6717457	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6719114	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6719278	1.00[ASN][1000 genomes]
rs6720483	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6721168	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723014	0.91[AFR][1000 genomes]
rs6725096	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6732113	1.00[ASN][1000 genomes]
rs6732250	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6732256	1.00[ASN][1000 genomes]
rs6739792	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744488	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6752779	0.84[AMR][1000 genomes]
rs6754660	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759567	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72946169	1.00[ASN][1000 genomes]
rs7559715	1.00[ASN][1000 genomes]
rs7566603	1.00[ASN][1000 genomes]
rs7566686	1.00[ASN][1000 genomes]
rs7568452	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7570297	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7573334	1.00[ASN][1000 genomes]
rs7573583	1.00[ASN][1000 genomes]
rs7582179	0.91[AFR][1000 genomes]
rs7585952	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7588049	0.91[AFR][1000 genomes]
rs7588444	1.00[ASN][1000 genomes]
rs7589927	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7594073	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7601132	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7604299	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604668	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7607073	0.94[AFR][1000 genomes]
rs7608135	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9288001	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935426	0.91[AFR][1000 genomes]
rs952034	1.00[ASN][1000 genomes]
rs9789580	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9917193	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9917333	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941681	1.00[ASN][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
rs6741974	AGPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178280400-178296000	Weak transcription	Small Intestine	intestine
2	chr2:178284600-178295800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:178287000-178296800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:178287200-178300000	Weak transcription	Hela-S3	cervix
5	chr2:178287200-178310600	Weak transcription	Stomach Mucosa	stomach
6	chr2:178287600-178314200	Weak transcription	Gastric	stomach
7	chr2:178288000-178297600	Weak transcription	HUVEC	blood vessel
8	chr2:178289400-178299400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:178291000-178299400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:178291600-178299200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr2:178291800-178299000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr2:178291800-178299200	ZNF genes & repeats	Primary B cells from cord blood	blood
13	chr2:178292600-178296000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:178292800-178296000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:178292800-178299400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr2:178293000-178295600	Strong transcription	Primary T cells from cord blood	blood
17	chr2:178293600-178298800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr2:178293800-178298800	ZNF genes & repeats	Dnd41	blood
19	chr2:178293800-178299000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:178294000-178295600	Enhancers	HMEC	breast
21	chr2:178294000-178296600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:178294000-178297000	ZNF genes & repeats	Fetal Thymus	thymus
23	chr2:178294000-178297800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
24	chr2:178294000-178299400	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr2:178294200-178295600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:178294200-178295600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:178294200-178295600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:178294200-178295600	Genic enhancers	HepG2	liver
29	chr2:178294200-178295600	Enhancers	NHDF-Ad	bronchial
30	chr2:178294200-178295600	Enhancers	Osteobl	bone
31	chr2:178294200-178297000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:178294200-178297800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:178294200-178297800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr2:178294200-178298400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
35	chr2:178294200-178299400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:178294400-178296000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr2:178294400-178296000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr2:178294400-178296800	ZNF genes & repeats	Placenta	Placenta
39	chr2:178294400-178298800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
40	chr2:178294600-178296400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
41	chr2:178294800-178295600	ZNF genes & repeats	K562	blood
42	chr2:178294800-178296400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
43	chr2:178294800-178296400	Weak transcription	Brain Anterior Caudate	brain
44	chr2:178295000-178295800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:178295000-178296000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr2:178295000-178296200	Weak transcription	Colonic Mucosa	Colon
47	chr2:178295000-178296600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:178295000-178297000	Weak transcription	Fetal Kidney	kidney
49	chr2:178295000-178297400	Weak transcription	Ovary	ovary
50	chr2:178295200-178295600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links