Variant report

Variant	rs10865341
Chromosome Location	chr2:63824050-63824051
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr2:63823743-63824113	HepG2	liver:	n/a	chr2:63823950-63823965 chr2:63823915-63823923
2	HNF4G	chr2:63823721-63824104	HepG2	liver:	n/a	chr2:63823915-63823923
3	POLR2A	chr2:63820532-63825081	K562	blood:	n/a	n/a
4	TEAD4	chr2:63823555-63824145	HepG2	liver:	n/a	n/a
5	HNF4A	chr2:63823749-63824102	HepG2	liver:	n/a	chr2:63823950-63823965 chr2:63823915-63823923
6	EP300	chr2:63823563-63824158	HepG2	liver:	n/a	chr2:63823726-63823740 chr2:63823916-63823926
7	HDAC2	chr2:63823565-63824080	HepG2	liver:	n/a	chr2:63823739-63823753 chr2:63823916-63823925
8	MYBL2	chr2:63823582-63824077	HepG2	liver:	n/a	n/a
9	FOXA1	chr2:63823551-63824066	HepG2	liver:	n/a	n/a
10	FOXA1	chr2:63823570-63824195	HepG2	liver:	n/a	n/a
11	FOXA1	chr2:63823574-63824192	HepG2	liver:	n/a	n/a
12	EP300	chr2:63823649-63824083	HepG2	liver:	n/a	chr2:63823726-63823740 chr2:63823916-63823926
13	FOXA2	chr2:63823532-63824054	HepG2	liver:	n/a	n/a
14	ARID3A	chr2:63823642-63824213	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63814544..63817562-chr2:63819288..63824360,10	K562	blood:
2	chr2:63814652..63820726-chr2:63822860..63830564,18	K562	blood:

Variant related genes	Relation type
MDH1	TF binding region
ENSG00000143951	Chromatin interaction
ENSG00000014641	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10168545	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10176522	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1023820	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10469944	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10469945	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1082363	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10865337	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10865338	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10865339	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11125977	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125978	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs112194	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11693909	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11898615	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12105140	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1255	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12713494	0.82[EUR][1000 genomes]
rs12713496	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12990914	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1348803	0.84[AMR][1000 genomes]
rs1446564	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1446565	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1446569	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1550860	0.81[EUR][1000 genomes]
rs166384	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs171901	0.80[AMR][1000 genomes]
rs171902	0.80[AMR][1000 genomes]
rs174485	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs185499	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1867847	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1867849	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs187801	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs190519	0.84[EUR][1000 genomes]
rs196124	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs196125	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2028883	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2084200	0.81[EUR][1000 genomes]
rs2121350	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2121351	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2166494	0.83[EUR][1000 genomes]
rs2166497	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2305157	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2422011	0.83[EUR][1000 genomes]
rs2592388	0.84[AMR][1000 genomes]
rs2604613	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2604614	0.84[AMR][1000 genomes]
rs2604617	0.80[AMR][1000 genomes]
rs262470	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262471	0.82[EUR][1000 genomes]
rs262472	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262473	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262474	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262475	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262476	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262477	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262478	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262479	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262480	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262481	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262482	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262483	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262484	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262485	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262486	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs262487	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262488	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262489	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262490	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262491	0.82[AMR][1000 genomes]
rs262493	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262495	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262501	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262502	0.83[EUR][1000 genomes]
rs262503	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262504	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262505	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262506	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs262507	0.82[AMR][1000 genomes]
rs262509	0.84[AMR][1000 genomes]
rs262515	0.87[AMR][1000 genomes]
rs262516	0.81[AMR][1000 genomes]
rs262518	0.81[AMR][1000 genomes]
rs262519	0.81[AMR][1000 genomes]
rs262523	0.84[AMR][1000 genomes]
rs262528	0.80[AMR][1000 genomes]
rs262529	0.80[AMR][1000 genomes]
rs262530	0.80[AMR][1000 genomes]
rs262533	0.80[AMR][1000 genomes]
rs262536	0.80[AMR][1000 genomes]
rs262538	0.80[AMR][1000 genomes]
rs2901614	0.82[EUR][1000 genomes]
rs3980466	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4671065	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671067	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4671068	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4671069	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4671509	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671514	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671515	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671516	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4671517	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4671519	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546007	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6546009	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6546011	0.84[AMR][1000 genomes]
rs6546016	0.80[EUR][1000 genomes]
rs6546017	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6546018	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546019	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6706123	0.82[EUR][1000 genomes]
rs6708804	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6717031	0.83[EUR][1000 genomes]
rs6724160	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6732791	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6734648	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6736029	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6738190	0.82[EUR][1000 genomes]
rs6754730	0.83[EUR][1000 genomes]
rs68183503	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7563623	0.83[EUR][1000 genomes]
rs7570031	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7571017	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7571325	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7576316	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7577952	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7584404	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7606045	0.83[EUR][1000 genomes]
rs7607257	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7608470	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7608513	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs959195	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs964880	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs964903	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9789351	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs989527	0.82[AMR][1000 genomes];0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10865341	WDPCP	cis	Adipose Subcutaneous	GTEx
rs10865341	AC074289.1	cis	Whole Blood	GTEx
rs10865341	MDH1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63816600-63830200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:63816800-63831000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:63817000-63827000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:63817000-63827000	Weak transcription	Spleen	Spleen
5	chr2:63817000-63827400	Weak transcription	Lung	lung
6	chr2:63817000-63828800	Weak transcription	Pancreas	Pancrea
7	chr2:63817000-63830200	Weak transcription	Esophagus	oesophagus
8	chr2:63817000-63831800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:63817200-63828000	Weak transcription	Aorta	Aorta
10	chr2:63817200-63834400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:63817400-63831600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:63817600-63828600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:63818000-63834800	Strong transcription	Fetal Thymus	thymus
14	chr2:63818000-63835400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:63818400-63828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:63818400-63829800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:63818400-63831000	Weak transcription	Gastric	stomach
18	chr2:63818400-63831800	Weak transcription	Colonic Mucosa	Colon
19	chr2:63818400-63831800	Weak transcription	Small Intestine	intestine
20	chr2:63818600-63834800	Strong transcription	Primary T cells from cord blood	blood
21	chr2:63818600-63835800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:63818800-63831800	Weak transcription	Fetal Brain Male	brain
23	chr2:63818800-63832000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:63819000-63827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:63819200-63825800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:63819200-63835000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:63819400-63824200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:63819400-63827200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:63819400-63829200	Strong transcription	Fetal Muscle Leg	muscle
30	chr2:63819400-63834800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:63819600-63834800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:63819800-63829400	Strong transcription	Left Ventricle	heart
33	chr2:63820200-63834800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:63820200-63834800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:63820200-63835200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:63820400-63825000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:63820400-63828600	Strong transcription	Fetal Lung	lung
38	chr2:63820400-63829600	Strong transcription	HMEC	breast
39	chr2:63820400-63834600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:63820400-63834800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:63820400-63835000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:63820400-63835000	Strong transcription	Liver	Liver
43	chr2:63820600-63824800	Strong transcription	Primary B cells from cord blood	blood
44	chr2:63820600-63824800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr2:63820600-63825000	Genic enhancers	Adipose Nuclei	Adipose
46	chr2:63820600-63825200	Strong transcription	K562	blood
47	chr2:63820600-63826000	Strong transcription	NH-A	brain
48	chr2:63820600-63834200	Strong transcription	A549	lung
49	chr2:63820600-63834800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:63820600-63834800	Strong transcription	Placenta	Placenta

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