Variant report

Variant	rs11548929
Chromosome Location	chr2:86756381-86756382
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86752276..86754731-chr2:86755226..86757056,2	MCF-7	breast:
2	chr2:86755933..86757641-chr2:86759393..86762137,2	K562	blood:
3	chr2:86754212..86756941-chr2:86758517..86760046,2	K562	blood:

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

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

rs_ID	r²[population]
rs1030886	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1030887	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11127043	0.99[EUR][1000 genomes]
rs11890032	0.89[EUR][1000 genomes]
rs11891659	1.00[EUR][1000 genomes]
rs11899532	0.86[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	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027296	0.94[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	0.99[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	0.92[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	0.97[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	0.89[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	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59613942	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859947	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59895355	0.96[EUR][1000 genomes]
rs60073472	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60244636	0.91[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	0.89[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710780	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720414	0.96[EUR][1000 genomes]
rs6740863	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745875	0.91[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	0.91[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932380	0.97[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	0.83[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	0.99[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
rs11548929	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	chr2:86733000-86759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:86733400-86758600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:86734000-86784800	Weak transcription	Osteobl	bone
5	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:86737000-86761200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
8	chr2:86737400-86756800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:86737400-86757400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:86737600-86768400	Weak transcription	Ovary	ovary
12	chr2:86737800-86756400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:86738200-86772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:86738200-86772600	Weak transcription	Right Ventricle	heart
16	chr2:86738400-86759000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:86741400-86768400	Weak transcription	Psoas Muscle	Psoas
18	chr2:86746000-86768000	Weak transcription	Fetal Heart	heart
19	chr2:86748000-86756400	Weak transcription	Fetal Lung	lung
20	chr2:86748000-86757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:86748000-86758000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:86748000-86758000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:86748000-86758600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:86748000-86760600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:86748000-86770600	Weak transcription	Gastric	stomach
26	chr2:86748200-86759000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:86749200-86756600	Strong transcription	Primary B cells from cord blood	blood
28	chr2:86749400-86757000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:86749400-86772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:86749400-86775000	Weak transcription	NH-A	brain
31	chr2:86749600-86757800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:86750000-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:86750400-86773600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:86751200-86756600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:86751400-86756600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:86751600-86757000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:86751800-86756400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:86752400-86756800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:86752600-86756400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:86752600-86756400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:86752600-86756600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:86752600-86756600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:86752600-86756600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:86752800-86756400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:86752800-86756600	Strong transcription	Liver	Liver
46	chr2:86752800-86756800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:86753000-86756400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:86753000-86756400	Strong transcription	Fetal Muscle Leg	muscle
49	chr2:86753000-86756400	Strong transcription	Dnd41	blood
50	chr2:86753000-86756600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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