Variant report

Variant	rs308916
Chromosome Location	chr2:86859904-86859905
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86858001..86860361-chr2:86914805..86916543,2	MCF-7	breast:
2	chr2:86855492..86857596-chr2:86858665..86860258,2	MCF-7	breast:
3	chr2:86667556..86669335-chr2:86857955..86860721,2	MCF-7	breast:
4	chr2:86858947..86862298-chr2:86867270..86869681,3	MCF-7	breast:
5	chr2:86859149..86861871-chr2:86863895..86866961,3	MCF-7	breast:
6	chr2:86859015..86860770-chr2:86917771..86920536,2	MCF-7	breast:
7	chr2:86857369..86860425-chr2:86900280..86904256,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1629293	1.00[ASW][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes]
rs218059	0.96[AMR][1000 genomes]
rs308900	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs308910	1.00[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs308912	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs308914	0.84[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes]
rs308915	0.92[CEU][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs422240	0.84[ASW][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs4832045	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs689912	0.91[AMR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs308916	PTCD3	cis	cerebellum	SCAN
rs308916	VPS24	cis	parietal	SCAN
rs308916	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs308916	IMMT	cis	cerebellum	SCAN
rs308916	RNF103	cis	cerebellum	SCAN
rs308916	POLR1A	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86851000-86860400	Weak transcription	Lung	lung
2	chr2:86851200-86860400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:86851800-86860000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:86851800-86860400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:86853000-86860400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:86853200-86860000	Weak transcription	Brain Anterior Caudate	brain
7	chr2:86856000-86860200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:86856600-86860400	Weak transcription	Psoas Muscle	Psoas
9	chr2:86858400-86860600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:86858400-86860800	Enhancers	Fetal Intestine Large	intestine
11	chr2:86858600-86860200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr2:86858600-86860400	Enhancers	Placenta	Placenta
13	chr2:86858600-86860800	Flanking Active TSS	HepG2	liver
14	chr2:86858600-86861000	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:86858600-86861200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:86858600-86861200	Enhancers	Brain Germinal Matrix	brain
17	chr2:86858600-86861400	Enhancers	Fetal Muscle Leg	muscle
18	chr2:86858800-86860000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr2:86858800-86860200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr2:86858800-86860600	Enhancers	Fetal Brain Female	brain
21	chr2:86858800-86861200	Enhancers	Fetal Intestine Small	intestine
22	chr2:86859000-86860200	Flanking Active TSS	Liver	Liver
23	chr2:86859000-86860800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:86859000-86861200	Enhancers	Brain Hippocampus Middle	brain
25	chr2:86859200-86860000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:86859200-86860000	Weak transcription	Brain Angular Gyrus	brain
27	chr2:86859200-86860000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:86859200-86860200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:86859200-86860400	Weak transcription	Left Ventricle	heart
30	chr2:86859200-86860600	Weak transcription	Gastric	stomach
31	chr2:86859200-86860800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:86859200-86861400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:86859200-86861800	Enhancers	Fetal Brain Male	brain
34	chr2:86859400-86860200	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:86859400-86860200	Enhancers	NHEK	skin
36	chr2:86859400-86860600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:86859400-86861200	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:86859400-86863000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:86859600-86860000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:86859600-86860000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:86859600-86860000	Weak transcription	Pancreas	Pancrea
42	chr2:86859600-86860000	Enhancers	A549	lung
43	chr2:86859600-86860200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:86859600-86860200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:86859600-86860800	Enhancers	Colonic Mucosa	Colon
46	chr2:86859800-86860000	Weak transcription	Stomach Mucosa	stomach
47	chr2:86859800-86860200	Weak transcription	Brain Substantia Nigra	brain
48	chr2:86859800-86860200	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr2:86859800-86860400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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