Variant report

Variant	rs308915
Chromosome Location	chr2:86859298-86859299
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

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	chr2:86857823..86859880-chr2:86861018..86863511,2	MCF-7	breast:
7	chr2:86856951..86859444-chr2:86896714..86898569,2	MCF-7	breast:
8	chr2:86859015..86860770-chr2:86917771..86920536,2	MCF-7	breast:
9	chr2:86857369..86860425-chr2:86900280..86904256,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1015117	0.87[GIH][hapmap]
rs11127045	0.84[GIH][hapmap]
rs12614447	0.87[GIH][hapmap]
rs12615285	0.87[GIH][hapmap]
rs12714198	0.84[GIH][hapmap]
rs12987172	0.87[GIH][hapmap]
rs13015620	0.87[GIH][hapmap]
rs13034615	0.84[GIH][hapmap]
rs1629293	0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs218059	0.99[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2241803	0.87[GIH][hapmap]
rs308900	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs308902	0.87[GIH][hapmap]
rs308903	0.85[GIH][hapmap]
rs308910	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs308912	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs308914	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs308916	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]
rs3201448	0.87[GIH][hapmap]
rs3755002	0.87[GIH][hapmap]
rs422240	0.81[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4832045	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4832300	0.87[GIH][hapmap]
rs4832304	0.91[GIH][hapmap]
rs6738663	0.87[GIH][hapmap]
rs6750226	0.87[GIH][hapmap]
rs689912	0.95[AMR][1000 genomes]
rs9284788	0.87[GIH][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs308915	RNF103	cis	cerebellum	SCAN
rs308915	POLR1A	cis	cerebellum	SCAN
rs308915	MAT2A	cis	parietal	SCAN
rs308915	IMMT	cis	cerebellum	SCAN
rs308915	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs308915	PTCD3	cis	cerebellum	SCAN
rs308915	VPS24	cis	lymphoblastoid	seeQTL
rs308915	VPS24	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

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	chr2:86853000-86859400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:86853000-86859600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:86853000-86860400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:86853200-86860000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:86856000-86860200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:86856600-86860400	Weak transcription	Psoas Muscle	Psoas
11	chr2:86858400-86859800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr2:86858400-86860600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:86858400-86860800	Enhancers	Fetal Intestine Large	intestine
14	chr2:86858600-86859400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:86858600-86859400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:86858600-86859400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:86858600-86859400	Enhancers	HMEC	breast
18	chr2:86858600-86859400	Flanking Active TSS	NHEK	skin
19	chr2:86858600-86859600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:86858600-86859600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:86858600-86859600	Enhancers	Pancreas	Pancrea
22	chr2:86858600-86859600	Enhancers	HUVEC	blood vessel
23	chr2:86858600-86860200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:86858600-86860400	Enhancers	Placenta	Placenta
25	chr2:86858600-86860800	Flanking Active TSS	HepG2	liver
26	chr2:86858600-86861000	Enhancers	Primary hematopoietic stem cells	blood
27	chr2:86858600-86861200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:86858600-86861200	Enhancers	Brain Germinal Matrix	brain
29	chr2:86858600-86861400	Enhancers	Fetal Muscle Leg	muscle
30	chr2:86858800-86859400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:86858800-86859400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:86858800-86859600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr2:86858800-86859600	Active TSS	Colonic Mucosa	Colon
34	chr2:86858800-86859600	Flanking Active TSS	A549	lung
35	chr2:86858800-86860000	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:86858800-86860200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr2:86858800-86860600	Enhancers	Fetal Brain Female	brain
38	chr2:86858800-86861200	Enhancers	Fetal Intestine Small	intestine
39	chr2:86859000-86859400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr2:86859000-86859400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr2:86859000-86859400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:86859000-86859400	Enhancers	H9 Cell Line	embryonic stem cell
43	chr2:86859000-86859400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:86859000-86859400	Enhancers	Right Atrium	heart
45	chr2:86859000-86859400	Flanking Active TSS	Stomach Mucosa	stomach
46	chr2:86859000-86859600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:86859000-86860200	Flanking Active TSS	Liver	Liver
48	chr2:86859000-86860800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:86859000-86861200	Enhancers	Brain Hippocampus Middle	brain
50	chr2:86859200-86859400	Enhancers	Colon Smooth Muscle	Colon

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