Variant report

Variant	rs689912
Chromosome Location	chr2:86851792-86851793
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr2:86849788-86851821	A549	lung:	n/a	chr2:86851018-86851028 chr2:86851097-86851108 chr2:86851049-86851061 chr2:86850621-86850631 chr2:86850454-86850463

No.	Distal block	Cell Line	Cell type
1	chr2:86849761..86852664-chr2:86946875..86949825,4	MCF-7	breast:
2	chr2:86667874..86671580-chr2:86848738..86852940,5	K562	blood:
3	chr2:86676152..86678942-chr2:86849820..86852421,2	MCF-7	breast:
4	chr2:86849205..86851980-chr4:103788532..103791480,2	MCF-7	breast:
5	chr2:86850136..86852379-chr2:86973884..86976847,2	K562	blood:
6	chr2:86848500..86851973-chr2:86945425..86949651,4	MCF-7	breast:
7	chr2:86839004..86842325-chr2:86847581..86852030,6	MCF-7	breast:
8	chr2:86787885..86791617-chr2:86846945..86852237,10	MCF-7	breast:

Variant related genes	Relation type
RNF103	TF binding region
RNF103-CHMP3	TF binding region
ENSG00000115548	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000228363	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000153561	Chromatin interaction
ENSG00000249884	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12328637	0.84[ASN][1000 genomes]
rs1629293	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs218059	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs308900	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs308902	0.80[EUR][1000 genomes]
rs308910	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs308912	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs308914	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs308915	0.95[AMR][1000 genomes]
rs308916	0.91[AMR][1000 genomes]
rs422240	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832045	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4832304	0.84[ASN][1000 genomes]
rs7601115	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	esv3498261	chr2:86849516-86851839	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	esv3498262	chr2:86849516-86851839	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
6	esv3404473	chr2:86849666-86852214	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
7	nsv436305	chr2:86849862-86854021	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs689912	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86851000-86854800	Weak transcription	Gastric	stomach
2	chr2:86851000-86854800	Weak transcription	Small Intestine	intestine
3	chr2:86851000-86856400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:86851000-86860400	Weak transcription	Lung	lung
5	chr2:86851200-86852200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:86851200-86854800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:86851200-86858400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:86851200-86860400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:86851400-86851800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr2:86851400-86851800	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:86851400-86851800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:86851400-86851800	Enhancers	K562	blood
13	chr2:86851400-86852800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:86851400-86853000	Enhancers	Brain Angular Gyrus	brain
15	chr2:86851400-86853200	Enhancers	Stomach Mucosa	stomach
16	chr2:86851400-86855400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:86851600-86851800	Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr2:86851600-86851800	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:86851600-86852200	Enhancers	Brain Hippocampus Middle	brain
20	chr2:86851600-86852400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:86851600-86852600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:86851600-86852600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:86851600-86852600	Enhancers	Fetal Muscle Leg	muscle
24	chr2:86851600-86852600	Enhancers	HSMMtube	muscle
25	chr2:86851600-86852800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:86851600-86852800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:86851600-86852800	Enhancers	Colonic Mucosa	Colon
28	chr2:86851600-86852800	Enhancers	A549	lung
29	chr2:86851600-86853000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:86851600-86853000	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:86851600-86853000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:86851600-86853000	Enhancers	Brain Substantia Nigra	brain
33	chr2:86851600-86853000	Enhancers	HepG2	liver
34	chr2:86851600-86853200	Enhancers	Brain Anterior Caudate	brain
35	chr2:86851600-86854400	Weak transcription	Fetal Intestine Small	intestine
36	chr2:86851600-86854600	Weak transcription	Liver	Liver
37	chr2:86851600-86854600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:86851600-86854600	Weak transcription	Fetal Intestine Large	intestine
39	chr2:86851600-86854600	Weak transcription	Pancreas	Pancrea
40	chr2:86851600-86854600	Weak transcription	GM12878-XiMat	blood
41	chr2:86851600-86854800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:86851600-86855400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:86851600-86855400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:86851600-86856800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:86851600-86858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:86851600-86858600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:86851600-86858600	Weak transcription	HMEC	breast

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