Variant report

Variant	rs4255949
Chromosome Location	chr2:63678589-63678590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10168545	0.86[EUR][1000 genomes]
rs10170988	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10171223	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10176522	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1023820	0.86[EUR][1000 genomes]
rs10469944	0.84[EUR][1000 genomes]
rs10469945	0.84[EUR][1000 genomes]
rs1082363	0.81[EUR][1000 genomes]
rs10865337	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10865338	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10865339	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11125977	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125978	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11693047	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11693909	0.82[EUR][1000 genomes]
rs11898615	0.86[EUR][1000 genomes]
rs12105140	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1255	0.82[EUR][1000 genomes]
rs12713494	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12713496	0.86[EUR][1000 genomes]
rs12990914	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1356390	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1446564	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1446565	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1446569	0.84[EUR][1000 genomes]
rs1550860	0.81[EUR][1000 genomes]
rs166384	0.81[EUR][1000 genomes]
rs171901	0.81[AMR][1000 genomes]
rs171902	0.81[AMR][1000 genomes]
rs174485	0.81[EUR][1000 genomes]
rs1867847	0.84[EUR][1000 genomes]
rs1867849	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs187801	0.80[EUR][1000 genomes]
rs196124	0.80[EUR][1000 genomes]
rs196125	0.80[EUR][1000 genomes]
rs2028883	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2028887	0.86[EUR][1000 genomes]
rs2084200	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2121350	0.84[EUR][1000 genomes]
rs2121351	0.83[EUR][1000 genomes]
rs2166494	0.84[EUR][1000 genomes]
rs2166497	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2176415	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2292793	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2422011	0.84[EUR][1000 genomes]
rs2604613	0.82[EUR][1000 genomes]
rs2604617	0.81[AMR][1000 genomes]
rs262470	0.83[EUR][1000 genomes]
rs262472	0.82[EUR][1000 genomes]
rs262473	0.83[EUR][1000 genomes]
rs262475	0.80[EUR][1000 genomes]
rs262476	0.80[EUR][1000 genomes]
rs262477	0.81[EUR][1000 genomes]
rs262479	0.81[EUR][1000 genomes]
rs262480	0.80[EUR][1000 genomes]
rs262484	0.80[EUR][1000 genomes]
rs262485	0.80[EUR][1000 genomes]
rs262490	0.81[EUR][1000 genomes]
rs262493	0.83[EUR][1000 genomes]
rs262495	0.83[EUR][1000 genomes]
rs262501	0.81[EUR][1000 genomes]
rs262503	0.81[EUR][1000 genomes]
rs262504	0.80[EUR][1000 genomes]
rs262506	0.80[EUR][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	0.82[EUR][1000 genomes]
rs3980466	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671065	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4671067	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4671068	0.85[EUR][1000 genomes]
rs4671069	0.82[EUR][1000 genomes]
rs4671503	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671505	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671508	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671509	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671512	0.83[EUR][1000 genomes]
rs4671514	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4671515	0.86[EUR][1000 genomes]
rs4671516	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4671519	0.82[EUR][1000 genomes]
rs6546004	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6546005	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6546007	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6546009	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6546016	0.81[EUR][1000 genomes]
rs6546017	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6546018	0.84[EUR][1000 genomes]
rs6546019	0.84[EUR][1000 genomes]
rs6706123	0.83[EUR][1000 genomes]
rs6708804	0.84[EUR][1000 genomes]
rs6717031	0.84[EUR][1000 genomes]
rs6724160	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6732791	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6734648	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6736029	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6736411	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6738190	0.86[EUR][1000 genomes]
rs6754730	0.83[EUR][1000 genomes]
rs68183503	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7563623	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7570031	0.83[EUR][1000 genomes]
rs7571017	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7571325	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7576316	0.86[EUR][1000 genomes]
rs7577952	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7584404	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7607257	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7608470	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7608513	0.84[EUR][1000 genomes]
rs959195	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs964880	0.82[EUR][1000 genomes]
rs964903	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9789351	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs989527	0.86[AMR][1000 genomes];0.87[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
rs4255949	MDH1	cis	Adipose Subcutaneous	GTEx
rs4255949	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63631800-63681200	Weak transcription	Aorta	Aorta
2	chr2:63631800-63688000	Weak transcription	Right Ventricle	heart
3	chr2:63655000-63679000	Weak transcription	Primary T cells from cord blood	blood
4	chr2:63659200-63679200	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:63659600-63679000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:63662000-63698000	Weak transcription	Ovary	ovary
7	chr2:63662200-63681400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:63662800-63688000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:63666400-63688000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:63666600-63726800	Weak transcription	Gastric	stomach
11	chr2:63667000-63680600	Weak transcription	Adipose Nuclei	Adipose
12	chr2:63668200-63684800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:63673600-63697800	Weak transcription	Left Ventricle	heart
14	chr2:63674400-63693200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:63675800-63712000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:63677800-63678800	Weak transcription	Lung	lung
17	chr2:63677800-63680600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:63678000-63681400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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