Variant report

Variant	rs262489
Chromosome Location	chr2:63836267-63836268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63835075..63837932-chr2:63839225..63843249,3	K562	blood:
2	chr2:63835463..63837099-chr2:63837397..63839181,2	K562	blood:

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10168545	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10170988	0.84[EUR][1000 genomes]
rs10171223	0.86[EUR][1000 genomes]
rs10176522	0.88[EUR][1000 genomes]
rs1023820	0.89[EUR][1000 genomes]
rs10469944	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10469945	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1082363	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10865337	0.88[EUR][1000 genomes]
rs10865338	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865339	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10865341	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125977	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11125978	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs112194	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11693909	0.88[EUR][1000 genomes]
rs11898615	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12105140	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1255	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12713494	0.84[EUR][1000 genomes]
rs12713496	0.89[EUR][1000 genomes]
rs12990914	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1348803	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1348806	0.83[EUR][1000 genomes]
rs1356390	0.84[EUR][1000 genomes]
rs1374308	0.83[EUR][1000 genomes]
rs1446563	0.83[EUR][1000 genomes]
rs1446564	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446565	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446569	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1550860	0.88[EUR][1000 genomes]
rs166384	0.91[EUR][1000 genomes]
rs166385	0.82[EUR][1000 genomes]
rs171901	0.83[EUR][1000 genomes]
rs171902	0.83[EUR][1000 genomes]
rs174485	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs185499	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1867847	0.91[EUR][1000 genomes]
rs1867849	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs187801	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs190519	0.88[EUR][1000 genomes]
rs196124	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs196125	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2028883	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2028887	0.87[EUR][1000 genomes]
rs2084200	0.88[EUR][1000 genomes]
rs2121350	0.91[EUR][1000 genomes]
rs2121351	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2121353	0.83[EUR][1000 genomes]
rs2166494	0.90[EUR][1000 genomes]
rs2166497	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2176415	0.80[EUR][1000 genomes]
rs2292793	0.84[EUR][1000 genomes]
rs2305157	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2422011	0.90[EUR][1000 genomes]
rs2592386	0.83[EUR][1000 genomes]
rs2592388	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2604613	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2604614	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2604617	0.83[EUR][1000 genomes]
rs262470	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262471	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262472	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs262473	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262474	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs262475	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262476	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262477	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs262478	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262479	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs262480	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262481	0.90[EUR][1000 genomes]
rs262482	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262483	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262484	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262485	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262486	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262487	0.89[EUR][1000 genomes]
rs262488	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262490	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs262491	0.81[AMR][1000 genomes]
rs262493	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262494	0.81[EUR][1000 genomes]
rs262495	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262501	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs262502	0.89[EUR][1000 genomes]
rs262503	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs262504	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262505	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262506	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs262507	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262508	0.83[EUR][1000 genomes]
rs262509	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262510	0.83[EUR][1000 genomes]
rs262514	0.83[EUR][1000 genomes]
rs262515	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs262516	0.83[EUR][1000 genomes]
rs262518	0.83[EUR][1000 genomes]
rs262519	0.83[EUR][1000 genomes]
rs262520	0.83[EUR][1000 genomes]
rs262521	0.83[EUR][1000 genomes]
rs262523	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262524	0.83[EUR][1000 genomes]
rs262525	0.82[EUR][1000 genomes]
rs262526	0.83[EUR][1000 genomes]
rs262527	0.83[EUR][1000 genomes]
rs262528	0.83[EUR][1000 genomes]
rs262529	0.83[EUR][1000 genomes]
rs262530	0.83[EUR][1000 genomes]
rs262533	0.83[EUR][1000 genomes]
rs262536	0.83[EUR][1000 genomes]
rs262538	0.83[EUR][1000 genomes]
rs2901614	0.89[EUR][1000 genomes]
rs3980466	0.83[EUR][1000 genomes]
rs4671064	0.81[EUR][1000 genomes]
rs4671065	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671066	0.81[EUR][1000 genomes]
rs4671067	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671068	0.91[EUR][1000 genomes]
rs4671069	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4671503	0.83[EUR][1000 genomes]
rs4671505	0.84[EUR][1000 genomes]
rs4671508	0.84[EUR][1000 genomes]
rs4671509	0.84[EUR][1000 genomes]
rs4671512	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671514	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671515	0.89[EUR][1000 genomes]
rs4671516	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671517	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671519	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6546004	0.83[EUR][1000 genomes]
rs6546005	0.82[EUR][1000 genomes]
rs6546007	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546009	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546011	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6546016	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546017	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546018	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546019	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6706123	0.89[EUR][1000 genomes]
rs6708804	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6717031	0.90[EUR][1000 genomes]
rs6724160	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6732791	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6734648	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736029	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736411	0.83[EUR][1000 genomes]
rs6738190	0.89[EUR][1000 genomes]
rs6754730	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs68183503	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7563623	0.91[EUR][1000 genomes]
rs7570031	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7571017	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7571325	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7576316	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7577952	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7581630	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7584404	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7606045	0.91[EUR][1000 genomes]
rs7607257	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7608470	0.83[EUR][1000 genomes]
rs7608513	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs959195	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs964880	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs964903	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9789351	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs989527	0.81[AMR][1000 genomes];0.91[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	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
2	esv1792289	chr2:63812148-63900292	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs262489	MDH1	cis	Adipose Subcutaneous	GTEx
rs262489	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63821600-63843000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:63829200-63839800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:63833200-63840200	Weak transcription	NHEK	skin
4	chr2:63833400-63837200	Weak transcription	Esophagus	oesophagus
5	chr2:63833600-63840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:63833600-63840200	Weak transcription	Psoas Muscle	Psoas
7	chr2:63833600-63841800	Weak transcription	K562	blood
8	chr2:63834200-63842400	Weak transcription	A549	lung
9	chr2:63834400-63840400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:63834400-63840600	Weak transcription	HMEC	breast
11	chr2:63834400-63841200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:63834400-63841200	Weak transcription	Osteobl	bone
13	chr2:63834400-63841800	Weak transcription	HSMMtube	muscle
14	chr2:63834600-63836400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:63834600-63836400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:63834600-63836600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:63834600-63836800	Weak transcription	Fetal Intestine Large	intestine
18	chr2:63834600-63837000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:63834600-63838000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:63834600-63838000	Weak transcription	GM12878-XiMat	blood
21	chr2:63834600-63839000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:63834600-63839200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:63834600-63839200	Weak transcription	HepG2	liver
24	chr2:63834600-63840000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:63834600-63840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:63834600-63840600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:63834600-63840600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:63834600-63840600	Weak transcription	NH-A	brain
29	chr2:63834600-63841200	Weak transcription	HSMM	muscle
30	chr2:63834600-63841400	Weak transcription	NHDF-Ad	bronchial
31	chr2:63834600-63841600	Weak transcription	Hela-S3	cervix
32	chr2:63834800-63836400	Weak transcription	Primary T cells from cord blood	blood
33	chr2:63834800-63836400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:63834800-63836400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:63834800-63836400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:63834800-63836400	Weak transcription	Colonic Mucosa	Colon
37	chr2:63834800-63836400	Weak transcription	Fetal Brain Male	brain
38	chr2:63834800-63836400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:63834800-63836400	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:63834800-63836400	Weak transcription	Gastric	stomach
41	chr2:63834800-63836400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:63834800-63836400	Weak transcription	Spleen	Spleen
43	chr2:63834800-63836600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:63834800-63836600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:63834800-63836600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:63834800-63836600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:63834800-63836600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:63834800-63836600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:63834800-63836600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:63834800-63836800	Weak transcription	Fetal Kidney	kidney

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