Variant report

Variant	rs308912
Chromosome Location	chr2:86856522-86856523
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86855526..86858566-chr2:86929665..86933195,3	MCF-7	breast:
2	chr2:86849700..86853087-chr2:86854052..86858493,4	K562	blood:
3	chr2:86834891..86837645-chr2:86855817..86858466,2	MCF-7	breast:
4	chr2:86855492..86857596-chr2:86858665..86860258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1629293	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs218059	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs308900	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs308902	0.86[EUR][1000 genomes]
rs308903	0.83[EUR][1000 genomes]
rs308910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs308914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs308915	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs308916	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs422240	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4832045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62147239	0.85[EUR][1000 genomes]
rs689912	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs308912	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86851000-86860400	Weak transcription	Lung	lung
2	chr2:86851200-86858400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:86851200-86860400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:86851600-86856800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:86851600-86858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:86851600-86858600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:86851600-86858600	Weak transcription	HMEC	breast
8	chr2:86851800-86860000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:86851800-86860400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:86852400-86858600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:86852600-86858600	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:86852800-86857200	Weak transcription	Colonic Mucosa	Colon
13	chr2:86852800-86859000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:86853000-86859000	Weak transcription	Brain Angular Gyrus	brain
15	chr2:86853000-86859400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:86853000-86859600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:86853000-86860400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:86853200-86860000	Weak transcription	Brain Anterior Caudate	brain
19	chr2:86854600-86856600	Enhancers	Duodenum Mucosa	Duodenum
20	chr2:86854600-86858000	Enhancers	Fetal Intestine Large	intestine
21	chr2:86854800-86858400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:86855400-86858400	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr2:86855600-86858600	Weak transcription	Gastric	stomach
24	chr2:86855600-86858600	Weak transcription	Pancreas	Pancrea
25	chr2:86855600-86858800	Weak transcription	Small Intestine	intestine
26	chr2:86855800-86859000	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:86856000-86857200	Enhancers	HepG2	liver
28	chr2:86856000-86860200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:86856200-86857600	Enhancers	Liver	Liver
30	chr2:86856200-86857800	Enhancers	Fetal Intestine Small	intestine
31	chr2:86856200-86858000	Enhancers	Stomach Mucosa	stomach
32	chr2:86856200-86858600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:86856200-86858600	Weak transcription	A549	lung
34	chr2:86856400-86856600	Enhancers	Sigmoid Colon	Sigmoid Colon

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