Variant report

Variant	rs57291816
Chromosome Location	chr2:86671868-86671869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86670537..86672265-chr2:86924211..86926595,2	MCF-7	breast:
2	chr2:86670380..86672664-chr2:86788557..86791421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228363	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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1518810	0.88[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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633268	0.86[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56055358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56085540	0.96[EUR][1000 genomes]
rs56169889	0.97[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56347930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56378606	0.82[EUR][1000 genomes]
rs57836876	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58091125	0.87[EUR][1000 genomes]
rs58361202	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58829418	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59026369	0.87[EUR][1000 genomes]
rs59183618	0.90[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930323	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930336	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930340	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930362	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930364	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930369	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930387	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930396	0.95[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
rs57291816	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	chr2:86669200-86672000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr2:86669800-86678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:86669800-86679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:86670000-86672800	Enhancers	Small Intestine	intestine
5	chr2:86670000-86678200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:86670000-86684200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:86670200-86672800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr2:86670400-86676400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:86670400-86693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:86670600-86672000	Genic enhancers	Thymus	Thymus
11	chr2:86670600-86672200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:86670600-86672600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:86670600-86672800	Genic enhancers	Adipose Nuclei	Adipose
14	chr2:86670600-86672800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr2:86670600-86673000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:86670600-86674000	Strong transcription	Placenta	Placenta
17	chr2:86670600-86674200	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr2:86670600-86675200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:86670600-86676400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:86670800-86672000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:86670800-86672200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:86670800-86672800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:86670800-86674200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr2:86670800-86675800	Weak transcription	HUVEC	blood vessel
25	chr2:86670800-86676200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:86670800-86676400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:86670800-86676600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:86670800-86677200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:86670800-86678600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:86670800-86681000	Weak transcription	Stomach Mucosa	stomach
31	chr2:86670800-86684200	Weak transcription	Colonic Mucosa	Colon
32	chr2:86671000-86672000	Enhancers	Brain Angular Gyrus	brain
33	chr2:86671000-86672200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:86671000-86672400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:86671000-86672400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:86671000-86672400	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr2:86671000-86672400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:86671000-86672600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:86671000-86672600	Weak transcription	Fetal Intestine Large	intestine
40	chr2:86671000-86672800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:86671000-86672800	Genic enhancers	Fetal Lung	lung
42	chr2:86671000-86673000	Enhancers	Brain Substantia Nigra	brain
43	chr2:86671000-86673000	Enhancers	Rectal Smooth Muscle	rectum
44	chr2:86671000-86673200	Enhancers	Hela-S3	cervix
45	chr2:86671000-86673400	Enhancers	Brain Hippocampus Middle	brain
46	chr2:86671000-86673600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:86671000-86673800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:86671000-86676800	Weak transcription	NH-A	brain
49	chr2:86671000-86676800	Weak transcription	Osteobl	bone
50	chr2:86671000-86677200	Weak transcription	Fetal Kidney	kidney

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