Variant report

Variant	rs3980466
Chromosome Location	chr2:63689185-63689186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10168545	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10170988	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171223	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176522	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1023820	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10469944	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10469945	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1082363	0.88[EUR][1000 genomes]
rs10865337	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10865338	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10865339	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865341	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11125977	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11125978	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs112194	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11693047	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11693909	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11898615	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12105140	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1255	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12713494	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713496	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12990914	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1348803	0.85[AMR][1000 genomes]
rs1348806	0.80[AMR][1000 genomes]
rs1356390	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374308	0.80[AMR][1000 genomes]
rs1446564	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1446565	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1446569	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1550860	0.86[EUR][1000 genomes]
rs166384	0.88[EUR][1000 genomes]
rs171901	0.81[AMR][1000 genomes]
rs171902	0.81[AMR][1000 genomes]
rs174485	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs185499	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1867847	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1867849	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs187801	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs190519	0.83[EUR][1000 genomes]
rs196124	0.87[EUR][1000 genomes]
rs196125	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2028883	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2028887	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2084200	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121350	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2121351	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2166494	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2166497	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2176415	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292793	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305157	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2422011	0.89[EUR][1000 genomes]
rs2592386	0.80[AMR][1000 genomes]
rs2592388	0.85[AMR][1000 genomes]
rs2604613	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2604614	0.85[AMR][1000 genomes]
rs2604617	0.81[AMR][1000 genomes]
rs262470	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262471	0.83[EUR][1000 genomes]
rs262472	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262473	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262474	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262475	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262476	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262477	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262478	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262479	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262480	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262481	0.85[EUR][1000 genomes]
rs262482	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262483	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262484	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262485	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262486	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262487	0.86[EUR][1000 genomes]
rs262488	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262489	0.83[EUR][1000 genomes]
rs262490	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262493	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262495	0.88[EUR][1000 genomes]
rs262501	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs262502	0.85[EUR][1000 genomes]
rs262503	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262504	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262505	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262506	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262507	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262509	0.81[AMR][1000 genomes]
rs262515	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262520	0.80[AMR][1000 genomes]
rs262521	0.80[AMR][1000 genomes]
rs262523	0.85[AMR][1000 genomes]
rs262524	0.80[AMR][1000 genomes]
rs262525	0.80[AMR][1000 genomes]
rs262528	0.81[AMR][1000 genomes]
rs262529	0.81[AMR][1000 genomes]
rs262530	0.81[AMR][1000 genomes]
rs262533	0.81[AMR][1000 genomes]
rs262536	0.81[AMR][1000 genomes]
rs262538	0.81[AMR][1000 genomes]
rs2901614	0.88[EUR][1000 genomes]
rs4255949	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671065	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671067	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671068	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671069	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671503	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671505	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671508	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671512	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671514	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671515	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671516	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671517	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4671519	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6546004	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546005	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546007	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6546009	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6546011	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6546016	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6546017	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6546018	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6546019	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706123	0.89[EUR][1000 genomes]
rs6708804	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6717031	0.89[EUR][1000 genomes]
rs6724160	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6732791	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6734648	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736029	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736411	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738190	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6754730	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68183503	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7563623	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7570031	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7571017	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7571325	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7576316	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7577952	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7581630	0.81[EUR][1000 genomes]
rs7584404	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606045	0.85[EUR][1000 genomes]
rs7607257	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7608470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608513	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs959195	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs964880	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs964903	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9789351	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs989527	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv874235	chr2:63622470-63709708	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3980466	MDH1	cis	Adipose Subcutaneous	GTEx
rs3980466	WDPCP	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63662000-63698000	Weak transcription	Ovary	ovary
2	chr2:63666600-63726800	Weak transcription	Gastric	stomach
3	chr2:63673600-63697800	Weak transcription	Left Ventricle	heart
4	chr2:63674400-63693200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:63675800-63712000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:63680400-63698400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:63680600-63705800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:63681600-63717800	Weak transcription	Aorta	Aorta
9	chr2:63682400-63717600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:63683400-63712800	Weak transcription	Fetal Thymus	thymus
11	chr2:63684600-63698800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:63684800-63695400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:63685800-63692800	Weak transcription	Fetal Heart	heart
14	chr2:63686000-63704600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:63686200-63698400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:63686600-63693000	Weak transcription	NH-A	brain
17	chr2:63686600-63706800	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:63686800-63692000	Strong transcription	Adipose Nuclei	Adipose
19	chr2:63687000-63693200	Weak transcription	Brain Angular Gyrus	brain
20	chr2:63687400-63692200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:63687400-63701000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:63687600-63689600	Weak transcription	Fetal Intestine Large	intestine
23	chr2:63687600-63713200	Weak transcription	Fetal Kidney	kidney
24	chr2:63688000-63692000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:63688200-63690400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:63688400-63690200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:63688600-63689800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:63688600-63690600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr2:63688600-63692400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:63688600-63696400	Weak transcription	Fetal Stomach	stomach
31	chr2:63688600-63704600	Weak transcription	Right Ventricle	heart
32	chr2:63688600-63705000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:63688600-63727800	Weak transcription	Primary B cells from cord blood	blood
34	chr2:63688800-63690200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:63688800-63691800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:63688800-63700600	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:63688800-63701800	Weak transcription	Fetal Lung	lung
38	chr2:63688800-63711000	Weak transcription	Brain Anterior Caudate	brain
39	chr2:63688800-63723000	Weak transcription	Liver	Liver
40	chr2:63689000-63689400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:63689000-63689600	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:63689000-63689800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:63689000-63689800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:63689000-63690000	Weak transcription	Primary T cells from cord blood	blood
45	chr2:63689000-63690000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:63689000-63690000	Weak transcription	Dnd41	blood
47	chr2:63689000-63690000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr2:63689000-63690600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:63689000-63700600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:63689000-63712000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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