Variant report

Variant	rs1030886
Chromosome Location	chr2:86755546-86755547
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86752024..86755712-chr2:86758517..86761265,3	K562	blood:
2	chr2:86752276..86754731-chr2:86755226..86757056,2	MCF-7	breast:
3	chr2:86754212..86756941-chr2:86758517..86760046,2	K562	blood:
4	chr2:86743323..86745032-chr2:86753355..86755938,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1030887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11127043	0.99[EUR][1000 genomes]
rs11548929	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11890032	0.89[EUR][1000 genomes]
rs11891659	1.00[EUR][1000 genomes]
rs11899532	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437614	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518808	0.91[EUR][1000 genomes]
rs1518810	0.89[EUR][1000 genomes]
rs1518812	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027265	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027270	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027280	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027296	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34605051	0.89[EUR][1000 genomes]
rs34633268	0.91[EUR][1000 genomes]
rs55688177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55708352	1.00[EUR][1000 genomes]
rs55828608	0.91[EUR][1000 genomes]
rs56055358	0.89[EUR][1000 genomes]
rs56085540	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56169889	0.91[EUR][1000 genomes]
rs56211578	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56227180	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56242451	0.89[EUR][1000 genomes]
rs56347930	0.91[EUR][1000 genomes]
rs56378606	0.90[EUR][1000 genomes]
rs57291816	0.91[EUR][1000 genomes]
rs57836876	0.89[EUR][1000 genomes]
rs58091125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58361202	0.91[EUR][1000 genomes]
rs58829418	0.89[EUR][1000 genomes]
rs59026369	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59183618	0.87[EUR][1000 genomes]
rs59255035	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59336972	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59521243	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59613942	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859947	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59895355	0.96[EUR][1000 genomes]
rs60073472	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60244636	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60304516	0.91[EUR][1000 genomes]
rs60717666	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60796561	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60810860	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs61028062	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61465748	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61547860	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720414	0.96[EUR][1000 genomes]
rs6740863	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745875	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930315	0.91[EUR][1000 genomes]
rs72930323	0.91[EUR][1000 genomes]
rs72930336	0.91[EUR][1000 genomes]
rs72930340	0.91[EUR][1000 genomes]
rs72930349	0.91[EUR][1000 genomes]
rs72930361	0.91[EUR][1000 genomes]
rs72930362	0.91[EUR][1000 genomes]
rs72930364	0.91[EUR][1000 genomes]
rs72930369	0.91[EUR][1000 genomes]
rs72930387	0.89[EUR][1000 genomes]
rs72930396	0.87[EUR][1000 genomes]
rs72930400	0.87[EUR][1000 genomes]
rs72932307	0.89[EUR][1000 genomes]
rs72932310	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932311	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932316	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932319	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932336	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932350	1.00[EUR][1000 genomes]
rs72932358	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932364	1.00[EUR][1000 genomes]
rs72932369	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932380	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73949838	0.90[EUR][1000 genomes]
rs73949839	0.90[EUR][1000 genomes]
rs7562493	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7585722	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7586028	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604179	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7608800	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs1030886	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
3	chr2:86733000-86759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86733400-86758600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:86734000-86784800	Weak transcription	Osteobl	bone
6	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:86737000-86761200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
9	chr2:86737400-86756800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:86737400-86757400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:86737600-86768400	Weak transcription	Ovary	ovary
13	chr2:86737800-86756400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:86738200-86756200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:86738200-86772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:86738200-86772600	Weak transcription	Right Ventricle	heart
18	chr2:86738400-86759000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:86741400-86768400	Weak transcription	Psoas Muscle	Psoas
20	chr2:86742400-86755600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:86744000-86755600	Weak transcription	Fetal Brain Female	brain
22	chr2:86746000-86768000	Weak transcription	Fetal Heart	heart
23	chr2:86748000-86755800	Weak transcription	Spleen	Spleen
24	chr2:86748000-86756400	Weak transcription	Fetal Lung	lung
25	chr2:86748000-86757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:86748000-86758000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:86748000-86758000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:86748000-86758600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:86748000-86760600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:86748000-86770600	Weak transcription	Gastric	stomach
31	chr2:86748200-86759000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:86749000-86755800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:86749200-86756600	Strong transcription	Primary B cells from cord blood	blood
34	chr2:86749400-86757000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:86749400-86772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:86749400-86775000	Weak transcription	NH-A	brain
37	chr2:86749600-86757800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:86750000-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:86750400-86755800	Weak transcription	Aorta	Aorta
40	chr2:86750400-86773600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:86751200-86756600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:86751400-86756600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:86751600-86757000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:86751800-86756400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:86752400-86756800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:86752600-86756400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:86752600-86756400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:86752600-86756600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:86752600-86756600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:86752600-86756600	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links