Variant report

Variant	rs1465813
Chromosome Location	chr2:86726094-86726095
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86720341..86722407-chr2:86724543..86726613,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1015117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10180036	0.93[CEU][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs10184879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10187880	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];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1020306	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11127045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11127046	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1137684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676576	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684230	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11689330	0.80[AFR][1000 genomes]
rs12613282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12614447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12623509	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs12714184	0.84[EUR][1000 genomes]
rs12714186	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12714188	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12714190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12714198	0.96[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12714199	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12987172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13015620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs13034615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13390713	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13408041	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13429696	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1518807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1629293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2241803	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292887	0.96[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2367574	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088046	0.81[ASN][1000 genomes]
rs3201448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770058	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422240	0.85[JPT][hapmap]
rs4832040	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832041	0.81[AMR][1000 genomes]
rs4832296	0.83[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832299	0.80[EUR][1000 genomes]
rs4832300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4832304	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs62150269	0.82[EUR][1000 genomes]
rs6725080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6750226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6752371	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7369138	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557796	0.88[CHB][hapmap]
rs7568840	0.88[CHB][hapmap]
rs7584882	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7593151	0.83[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8179729	0.83[ASN][1000 genomes]
rs9284788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs958561	0.96[CEU][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs9789777	0.88[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1465813	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
8	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
11	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
12	chr2:86704800-86726400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:86704800-86726600	Strong transcription	NHDF-Ad	bronchial
14	chr2:86708800-86726600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:86709200-86726600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:86712800-86726600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:86713400-86727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:86717200-86726600	Weak transcription	Pancreas	Pancrea
20	chr2:86717400-86726600	Weak transcription	Stomach Mucosa	stomach
21	chr2:86718800-86726600	Weak transcription	Gastric	stomach
22	chr2:86718800-86726600	Weak transcription	Right Ventricle	heart
23	chr2:86719400-86726600	Weak transcription	Spleen	Spleen
24	chr2:86719800-86726600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:86719800-86726800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:86719800-86726800	Strong transcription	Liver	Liver
27	chr2:86719800-86726800	Weak transcription	Esophagus	oesophagus
28	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
29	chr2:86720400-86726600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr2:86720400-86727000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:86721400-86728000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr2:86722000-86726400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:86722000-86727200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:86722200-86727000	Strong transcription	Fetal Stomach	stomach
35	chr2:86722200-86730600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:86722400-86726400	Weak transcription	Small Intestine	intestine
37	chr2:86722600-86726400	Strong transcription	Fetal Brain Female	brain
38	chr2:86723000-86726600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:86723000-86726600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:86723400-86726400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:86723400-86726600	Strong transcription	Adipose Nuclei	Adipose
42	chr2:86723800-86726600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:86723800-86726600	Strong transcription	Brain Germinal Matrix	brain
44	chr2:86723800-86727000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr2:86723800-86728000	Strong transcription	Colon Smooth Muscle	Colon
46	chr2:86724000-86726400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:86724000-86726600	Strong transcription	Fetal Thymus	thymus
48	chr2:86724000-86726800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:86724000-86727200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:86724000-86728000	Strong transcription	Muscle Satellite Cultured Cells	--

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