Variant report

Variant	rs56227180
Chromosome Location	chr2:86787598-86787599
allele	C/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	POLR2A	chr2:86787509-86787661	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000228363	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1030886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1030887	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11127043	0.95[EUR][1000 genomes]
rs11548929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11890032	0.85[EUR][1000 genomes]
rs11891659	0.96[EUR][1000 genomes]
rs11899532	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1437614	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1518808	0.87[EUR][1000 genomes]
rs1518810	0.85[EUR][1000 genomes]
rs1518812	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027265	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027270	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027280	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17027296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34605051	0.85[EUR][1000 genomes]
rs34633268	0.87[EUR][1000 genomes]
rs55688177	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55708352	0.96[EUR][1000 genomes]
rs55828608	0.87[EUR][1000 genomes]
rs56055358	0.85[EUR][1000 genomes]
rs56085540	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56169889	0.87[EUR][1000 genomes]
rs56211578	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56242451	0.85[EUR][1000 genomes]
rs56347930	0.87[EUR][1000 genomes]
rs56378606	0.94[EUR][1000 genomes]
rs57291816	0.87[EUR][1000 genomes]
rs57836876	0.85[EUR][1000 genomes]
rs58091125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58361202	0.87[EUR][1000 genomes]
rs58829418	0.85[EUR][1000 genomes]
rs59026369	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59183618	0.83[EUR][1000 genomes]
rs59255035	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59336972	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59521243	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59613942	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59859947	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59895355	1.00[EUR][1000 genomes]
rs60073472	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60244636	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60304516	0.87[EUR][1000 genomes]
rs60717666	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60796561	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60810860	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61028062	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61465748	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61547860	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6710780	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6720414	1.00[EUR][1000 genomes]
rs6740863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6745875	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72930315	0.87[EUR][1000 genomes]
rs72930323	0.87[EUR][1000 genomes]
rs72930336	0.87[EUR][1000 genomes]
rs72930340	0.87[EUR][1000 genomes]
rs72930349	0.87[EUR][1000 genomes]
rs72930361	0.87[EUR][1000 genomes]
rs72930362	0.87[EUR][1000 genomes]
rs72930364	0.87[EUR][1000 genomes]
rs72930369	0.87[EUR][1000 genomes]
rs72930387	0.85[EUR][1000 genomes]
rs72930396	0.83[EUR][1000 genomes]
rs72930400	0.83[EUR][1000 genomes]
rs72932307	0.85[EUR][1000 genomes]
rs72932310	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932311	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932316	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932319	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932336	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932350	0.96[EUR][1000 genomes]
rs72932358	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932364	0.96[EUR][1000 genomes]
rs72932369	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932380	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73949838	0.94[EUR][1000 genomes]
rs73949839	0.94[EUR][1000 genomes]
rs7562493	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7585722	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7586028	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7604179	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7608800	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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	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
rs56227180	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:86753800-86788400	Weak transcription	HSMM	muscle
3	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:86756600-86789200	Weak transcription	Aorta	Aorta
5	chr2:86761200-86788600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:86761200-86788800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:86771200-86788400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:86774200-86788200	Weak transcription	Adipose Nuclei	Adipose
9	chr2:86774400-86788800	Weak transcription	Fetal Lung	lung
10	chr2:86774600-86788200	Weak transcription	Hela-S3	cervix
11	chr2:86775200-86788200	Weak transcription	K562	blood
12	chr2:86775200-86788800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:86776800-86788800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:86777000-86787800	Weak transcription	Ovary	ovary
15	chr2:86777000-86788000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:86777400-86789200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:86777400-86789600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:86777600-86788000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:86777600-86788200	Weak transcription	Liver	Liver
20	chr2:86777600-86789200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:86777600-86789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:86777600-86789400	Weak transcription	Lung	lung
23	chr2:86777800-86787800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:86777800-86788400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:86777800-86789400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:86778200-86789000	Weak transcription	NHLF	lung
27	chr2:86779400-86788800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:86779400-86789400	Weak transcription	Placenta	Placenta
29	chr2:86780000-86788400	Weak transcription	HMEC	breast
30	chr2:86780200-86789000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:86780600-86788600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:86780800-86789400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:86780800-86789600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:86781200-86788800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:86781400-86788000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:86782000-86788400	Weak transcription	Fetal Kidney	kidney
37	chr2:86782400-86788400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:86782600-86788200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:86782600-86789000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr2:86782800-86788600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:86783000-86788200	Weak transcription	Dnd41	blood
42	chr2:86783000-86789200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:86783200-86789400	Weak transcription	Fetal Thymus	thymus
44	chr2:86784200-86788400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:86784200-86788400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:86784400-86788200	Weak transcription	NHEK	skin
47	chr2:86784400-86789400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:86784400-86789400	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:86784600-86788400	Weak transcription	Fetal Brain Female	brain
50	chr2:86784600-86789200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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