Variant report

Variant	rs10826425
Chromosome Location	chr10:28501117-28501118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10508736	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10740785	0.81[ASN][1000 genomes]
rs10740786	0.81[ASN][1000 genomes]
rs10763646	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10763647	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10763648	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10763649	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10763650	0.81[ASN][1000 genomes]
rs10763654	0.95[JPT][hapmap]
rs10763655	0.91[JPT][hapmap]
rs10826414	0.81[ASN][1000 genomes]
rs10826417	0.81[ASN][1000 genomes]
rs10826418	0.81[ASN][1000 genomes]
rs10826419	0.81[ASN][1000 genomes]
rs10826421	0.86[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10826422	0.81[ASN][1000 genomes]
rs10826424	0.83[ASN][1000 genomes]
rs10826435	0.95[JPT][hapmap]
rs11006915	0.83[ASN][1000 genomes]
rs11006917	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11006950	0.83[JPT][hapmap]
rs11006957	0.95[JPT][hapmap]
rs11006965	0.95[JPT][hapmap]
rs11006970	0.95[JPT][hapmap]
rs1148175	0.86[JPT][hapmap]
rs12049636	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12221232	0.81[ASN][1000 genomes]
rs12248472	0.83[ASN][1000 genomes]
rs12251587	0.90[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs12255686	0.86[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1418757	0.95[JPT][hapmap]
rs1418759	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs17758855	0.95[JPT][hapmap]
rs1824172	0.81[ASN][1000 genomes]
rs1870097	1.00[JPT][hapmap]
rs1870098	0.82[JPT][hapmap]
rs1937807	0.88[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1937808	0.88[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1937809	0.88[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2100615	0.95[JPT][hapmap]
rs2607539	0.81[ASN][1000 genomes]
rs2607542	0.81[ASN][1000 genomes]
rs2607543	0.81[ASN][1000 genomes]
rs2607544	0.81[ASN][1000 genomes]
rs2607545	0.80[ASN][1000 genomes]
rs2607546	0.80[ASN][1000 genomes]
rs2801833	0.80[ASN][1000 genomes]
rs2801835	0.81[ASN][1000 genomes]
rs2985521	0.80[ASN][1000 genomes]
rs2985535	0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2997210	0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs3847382	0.83[ASN][1000 genomes]
rs3901407	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3905706	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4018718	0.81[ASN][1000 genomes]
rs4568902	0.90[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs6481515	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs7067826	0.81[ASN][1000 genomes]
rs7068687	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs7088465	0.95[JPT][hapmap]
rs7088552	0.90[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs7096944	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs72631847	0.81[ASN][1000 genomes]
rs7893311	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7913970	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs7915273	0.81[ASN][1000 genomes]
rs7922685	0.90[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv6188	chr10:28489076-28514068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10826425	MKX	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28467600-28525600	Weak transcription	Aorta	Aorta
2	chr10:28485600-28504400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:28487600-28529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr10:28489800-28504400	Weak transcription	Esophagus	oesophagus
5	chr10:28491200-28523200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:28492200-28504400	Weak transcription	Psoas Muscle	Psoas
7	chr10:28492200-28506800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:28492600-28506400	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:28492600-28507200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:28497400-28503800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr10:28497400-28506600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:28497800-28501400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr10:28497800-28503400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:28498000-28501400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr10:28498000-28505600	Weak transcription	HSMMtube	muscle
16	chr10:28498000-28506600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:28498200-28504400	Weak transcription	Lung	lung
18	chr10:28498200-28506600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr10:28498200-28531200	Weak transcription	Primary B cells from cord blood	blood
20	chr10:28498200-28537000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:28498400-28501200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr10:28498400-28501600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr10:28498400-28503200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:28498400-28504000	Weak transcription	Fetal Intestine Small	intestine
25	chr10:28498400-28504400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:28499000-28505000	Weak transcription	HepG2	liver
27	chr10:28499000-28506800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:28499000-28507000	Weak transcription	Ovary	ovary
29	chr10:28499200-28501400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr10:28499400-28503000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:28500000-28501200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr10:28500000-28502600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr10:28500200-28501400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr10:28500200-28502200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr10:28500200-28503400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr10:28500400-28503200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:28500400-28506800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:28500600-28502400	Strong transcription	Primary T cells from cord blood	blood
39	chr10:28500600-28503600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr10:28500800-28501200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr10:28500800-28501600	Weak transcription	Stomach Mucosa	stomach
42	chr10:28500800-28503000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:28500800-28503000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr10:28500800-28503200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr10:28500800-28503400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr10:28501000-28501800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr10:28501000-28502200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:28501000-28503800	Strong transcription	Monocytes-CD14+_RO01746	blood

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