Variant report

Variant	rs10187880
Chromosome Location	chr2:86775189-86775190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1015117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10169746	0.94[ASN][1000 genomes]
rs10180036	0.93[CEU][hapmap];0.87[YRI][hapmap]
rs10184879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10187753	0.82[EUR][1000 genomes]
rs10188515	0.95[ASN][1000 genomes]
rs1020306	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10432704	0.96[ASN][1000 genomes]
rs1080551	0.94[ASN][1000 genomes]
rs11127045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11127046	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1137684	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11676576	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11684230	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11689330	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11689593	0.93[ASN][1000 genomes]
rs12328637	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12613282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12614447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12615285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs12714186	0.96[CEU][hapmap]
rs12714188	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12714190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12714198	0.96[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12714199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12987172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991654	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13015620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13034615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13390713	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13408041	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13429696	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1465813	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1518807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1629293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs218059	0.87[ASN][1000 genomes]
rs2241803	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292887	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs2367574	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3201448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34666164	0.94[ASN][1000 genomes]
rs3731812	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770058	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs422240	0.85[JPT][hapmap]
rs4832040	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4832041	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4832042	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832043	0.82[EUR][1000 genomes]
rs4832045	0.92[ASN][1000 genomes]
rs4832296	0.98[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832299	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4832302	0.94[ASN][1000 genomes]
rs4832303	0.82[EUR][1000 genomes]
rs4832304	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62147239	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6725080	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6728211	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6731025	0.92[ASN][1000 genomes]
rs6733569	0.82[EUR][1000 genomes]
rs6738663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6750226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7369138	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557796	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs7568840	0.88[CHB][hapmap]
rs7570640	0.94[ASN][1000 genomes]
rs7584882	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7593151	0.98[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7601115	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8179729	0.98[ASN][1000 genomes]
rs9284788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs958561	0.96[CEU][hapmap];0.85[YRI][hapmap]
rs9789777	0.81[ASN][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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv829488	chr2:86769108-86780946	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10187880	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86734000-86784800	Weak transcription	Osteobl	bone
2	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:86753800-86788400	Weak transcription	HSMM	muscle
5	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
6	chr2:86756600-86776200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:86756600-86779000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:86756600-86779000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:86756600-86784800	Weak transcription	Left Ventricle	heart
10	chr2:86756600-86789200	Weak transcription	Aorta	Aorta
11	chr2:86756800-86779400	Weak transcription	NHDF-Ad	bronchial
12	chr2:86761200-86788600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:86761200-86788800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:86761400-86779400	Weak transcription	NHEK	skin
15	chr2:86764600-86779600	Weak transcription	HMEC	breast
16	chr2:86768200-86785000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:86768800-86776000	Weak transcription	Ovary	ovary
18	chr2:86768800-86780000	Weak transcription	Small Intestine	intestine
19	chr2:86768800-86784200	Weak transcription	Psoas Muscle	Psoas
20	chr2:86768800-86785200	Weak transcription	Stomach Mucosa	stomach
21	chr2:86769400-86785600	Weak transcription	Fetal Heart	heart
22	chr2:86770000-86779000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:86770800-86776000	Weak transcription	Gastric	stomach
24	chr2:86771000-86777600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr2:86771200-86788400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:86771400-86779000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:86771400-86786200	Weak transcription	HSMMtube	muscle
28	chr2:86772200-86779000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:86772600-86776400	ZNF genes & repeats	Brain Germinal Matrix	brain
30	chr2:86772600-86777200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:86772800-86775400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr2:86772800-86778200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:86773000-86775200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:86773000-86775800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:86773000-86776000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:86773000-86776600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr2:86773000-86779000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:86773200-86776000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:86773200-86781400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:86773400-86775800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:86773400-86776000	Weak transcription	Pancreas	Pancrea
42	chr2:86773400-86776000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:86773400-86784200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:86773600-86775200	ZNF genes & repeats	Dnd41	blood
45	chr2:86773600-86775400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr2:86773600-86775800	Weak transcription	Colonic Mucosa	Colon
47	chr2:86773600-86779600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
48	chr2:86773800-86775200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:86773800-86775200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:86773800-86775200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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