Variant report

Variant	rs56347930
Chromosome Location	chr2:86683901-86683902
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86669725..86671528-chr2:86682298..86684898,2	MCF-7	breast:
2	chr2:86683189..86686593-chr2:86691402..86694661,3	K562	blood:
3	chr2:86683337..86686158-chr2:86788468..86790099,2	K562	blood:

Variant related genes	Relation type
ENSG00000228363	Chromatin interaction
ENSG00000115548	Chromatin interaction
ENSG00000115561	Chromatin interaction

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

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

rs_ID	r²[population]
rs1030886	0.91[EUR][1000 genomes]
rs1030887	0.91[EUR][1000 genomes]
rs11127043	0.90[EUR][1000 genomes]
rs11548929	0.91[EUR][1000 genomes]
rs11890032	0.81[EUR][1000 genomes]
rs11891659	0.91[EUR][1000 genomes]
rs11899532	0.96[EUR][1000 genomes]
rs1437614	0.93[EUR][1000 genomes]
rs1518808	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1518810	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1518812	0.96[EUR][1000 genomes]
rs17027265	0.96[EUR][1000 genomes]
rs17027270	0.96[EUR][1000 genomes]
rs17027280	0.91[EUR][1000 genomes]
rs17027296	0.87[EUR][1000 genomes]
rs34605051	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633268	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55688177	0.91[EUR][1000 genomes]
rs55708352	0.91[EUR][1000 genomes]
rs55828608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56055358	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56085540	0.96[EUR][1000 genomes]
rs56169889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56211578	0.85[EUR][1000 genomes]
rs56227180	0.87[EUR][1000 genomes]
rs56242451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56378606	0.82[EUR][1000 genomes]
rs57291816	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57836876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58091125	0.87[EUR][1000 genomes]
rs58361202	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58829418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59026369	0.87[EUR][1000 genomes]
rs59183618	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59255035	0.98[EUR][1000 genomes]
rs59336972	0.96[EUR][1000 genomes]
rs59521243	0.87[EUR][1000 genomes]
rs59613942	0.87[EUR][1000 genomes]
rs59859947	0.87[EUR][1000 genomes]
rs59895355	0.87[EUR][1000 genomes]
rs60073472	0.87[EUR][1000 genomes]
rs60244636	0.87[EUR][1000 genomes]
rs60304516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60717666	0.98[EUR][1000 genomes]
rs60796561	0.87[EUR][1000 genomes]
rs60810860	0.93[EUR][1000 genomes]
rs61028062	0.96[EUR][1000 genomes]
rs61465748	0.87[EUR][1000 genomes]
rs61547860	0.91[EUR][1000 genomes]
rs6710780	0.91[EUR][1000 genomes]
rs6720414	0.87[EUR][1000 genomes]
rs6740863	0.91[EUR][1000 genomes]
rs6745875	0.91[EUR][1000 genomes]
rs72930315	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930323	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930336	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930364	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930387	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930396	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72930400	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932307	0.98[EUR][1000 genomes]
rs72932310	0.96[EUR][1000 genomes]
rs72932311	0.96[EUR][1000 genomes]
rs72932316	0.96[EUR][1000 genomes]
rs72932319	0.96[EUR][1000 genomes]
rs72932336	0.91[EUR][1000 genomes]
rs72932350	0.91[EUR][1000 genomes]
rs72932358	0.91[EUR][1000 genomes]
rs72932364	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932369	0.91[EUR][1000 genomes]
rs72932380	0.87[EUR][1000 genomes]
rs73949838	0.82[EUR][1000 genomes]
rs73949839	0.82[EUR][1000 genomes]
rs7562493	0.91[EUR][1000 genomes]
rs7585722	0.87[EUR][1000 genomes]
rs7586028	0.87[EUR][1000 genomes]
rs7604179	0.91[EUR][1000 genomes]
rs7608800	0.91[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
rs56347930	VPS24	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86670000-86684200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:86670400-86693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:86670800-86684200	Weak transcription	Colonic Mucosa	Colon
4	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:86671200-86689400	Strong transcription	Primary B cells from cord blood	blood
6	chr2:86671400-86684200	Weak transcription	Gastric	stomach
7	chr2:86671400-86685600	Weak transcription	Esophagus	oesophagus
8	chr2:86671400-86687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:86671400-86725600	Strong transcription	A549	lung
11	chr2:86671600-86695400	Strong transcription	HSMM	muscle
12	chr2:86671600-86719800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
14	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
17	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:86674000-86685200	Weak transcription	Pancreas	Pancrea
19	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:86674600-86721400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr2:86674800-86695000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:86675400-86694600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:86675600-86692000	Strong transcription	Dnd41	blood
24	chr2:86676400-86693600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:86676400-86722600	Strong transcription	GM12878-XiMat	blood
26	chr2:86676600-86695600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:86676600-86721600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:86676800-86686000	Strong transcription	NH-A	brain
30	chr2:86676800-86686600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:86676800-86690600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:86676800-86698200	Strong transcription	Placenta	Placenta
33	chr2:86676800-86701000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:86676800-86703800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:86677000-86689200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:86677000-86689400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:86677000-86692000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:86677000-86705200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:86677200-86689200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr2:86677200-86708200	Strong transcription	HepG2	liver
41	chr2:86677200-86709200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:86677400-86685600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:86677800-86684200	Weak transcription	Lung	lung
44	chr2:86677800-86690400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:86677800-86691600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:86677800-86693200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:86678000-86693200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:86678200-86689000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr2:86679000-86684000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:86679400-86684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links