Variant report

Variant	rs10178917
Chromosome Location	chr2:86598365-86598366
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86593659..86596612-chr2:86598158..86600807,3	K562	blood:
2	chr2:86420778..86424048-chr2:86595325..86598515,3	MCF-7	breast:
3	chr2:86593659..86595230-chr2:86598158..86600807,2	K562	blood:
4	chr2:86421063..86423710-chr2:86595515..86598426,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10180036	0.81[AMR][1000 genomes]
rs10208989	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1113169	0.93[ASN][1000 genomes]
rs12617075	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714181	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12714183	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12714184	0.81[AMR][1000 genomes]
rs12714186	0.81[AMR][1000 genomes]
rs13035266	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13383096	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13420491	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1964089	0.85[EUR][1000 genomes]
rs2113607	1.00[ASN][1000 genomes]
rs2367237	0.85[AMR][1000 genomes]
rs4832278	0.91[ASN][1000 genomes]
rs4832279	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832280	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832282	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547677	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6716701	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs766285	0.85[EUR][1000 genomes]
rs908791	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs958561	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10178917	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86595800-86598800	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:86596000-86598400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:86596000-86598400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:86596000-86598600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:86596000-86598600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr2:86596000-86598600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:86596000-86598600	Weak transcription	Fetal Lung	lung
8	chr2:86596000-86599400	Weak transcription	Lung	lung
9	chr2:86596000-86599600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:86596000-86600200	Weak transcription	Psoas Muscle	Psoas
11	chr2:86596000-86600400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr2:86596200-86598600	Enhancers	Primary T cells from cord blood	blood
13	chr2:86596200-86598600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:86596400-86598400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:86596400-86598600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:86597400-86598400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:86597600-86598600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:86598000-86598600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:86598000-86599800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:86598000-86600400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:86598000-86600400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr2:86598200-86599800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:86598200-86600200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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