Variant report

Variant	rs60304516
Chromosome Location	chr2:86676508-86676509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86675470..86677064-chr2:86789067..86791804,2	K562	blood:
2	chr2:86676152..86678942-chr2:86849820..86852421,2	MCF-7	breast:
3	chr2:86675009..86676649-chr2:86692152..86693792,2	K562	blood:

Variant related genes	Relation type
ENSG00000228363	Chromatin interaction
ENSG00000115548	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000249884	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1518810	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	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633268	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55688177	0.91[EUR][1000 genomes]
rs55708352	0.91[EUR][1000 genomes]
rs55828608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56055358	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56085540	0.96[EUR][1000 genomes]
rs56169889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56211578	0.85[EUR][1000 genomes]
rs56227180	0.87[EUR][1000 genomes]
rs56242451	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56347930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56378606	0.82[EUR][1000 genomes]
rs57291816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57836876	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58091125	0.87[EUR][1000 genomes]
rs58361202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58829418	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59026369	0.87[EUR][1000 genomes]
rs59183618	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]
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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930349	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930369	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930387	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930396	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
rs60304516	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86669800-86678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:86669800-86679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:86670000-86678200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:86670000-86684200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:86670400-86693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:86670800-86676600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:86670800-86677200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:86670800-86678600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:86670800-86681000	Weak transcription	Stomach Mucosa	stomach
10	chr2:86670800-86684200	Weak transcription	Colonic Mucosa	Colon
11	chr2:86671000-86676800	Weak transcription	NH-A	brain
12	chr2:86671000-86676800	Weak transcription	Osteobl	bone
13	chr2:86671000-86677200	Weak transcription	Fetal Kidney	kidney
14	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:86671200-86677000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:86671200-86689400	Strong transcription	Primary B cells from cord blood	blood
17	chr2:86671400-86676800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:86671400-86676800	Weak transcription	NHDF-Ad	bronchial
19	chr2:86671400-86677200	Genic enhancers	HepG2	liver
20	chr2:86671400-86677400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr2:86671400-86678000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:86671400-86678200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:86671400-86684200	Weak transcription	Gastric	stomach
24	chr2:86671400-86685600	Weak transcription	Esophagus	oesophagus
25	chr2:86671400-86687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:86671400-86725600	Strong transcription	A549	lung
28	chr2:86671600-86676800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:86671600-86676800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:86671600-86677000	Weak transcription	NHLF	lung
31	chr2:86671600-86680800	Weak transcription	Fetal Brain Male	brain
32	chr2:86671600-86695400	Strong transcription	HSMM	muscle
33	chr2:86671600-86719800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
35	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:86671800-86676600	Weak transcription	HSMMtube	muscle
37	chr2:86671800-86680400	Weak transcription	Right Atrium	heart
38	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr2:86672000-86681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:86672400-86677200	Weak transcription	Fetal Brain Female	brain
41	chr2:86672600-86677200	Weak transcription	Brain Angular Gyrus	brain
42	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
43	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:86672800-86678800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:86672800-86680400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:86672800-86680600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:86673000-86677000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr2:86673000-86678600	Weak transcription	Spleen	Spleen
49	chr2:86673200-86676600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:86673200-86677200	Weak transcription	Hela-S3	cervix

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