Variant report

Variant	rs308900
Chromosome Location	chr2:86847269-86847270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86788265..86792368-chr2:86847223..86851122,9	MCF-7	breast:
2	chr2:86787885..86791617-chr2:86846945..86852237,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228363	Chromatin interaction
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10169746	0.82[ASN][1000 genomes]
rs10184584	0.81[ASN][1000 genomes]
rs10184879	0.82[ASN][1000 genomes]
rs10187753	0.81[ASN][1000 genomes]
rs10432704	0.81[ASN][1000 genomes]
rs1080551	0.82[ASN][1000 genomes]
rs11127047	0.81[ASN][1000 genomes]
rs11689330	0.82[ASN][1000 genomes]
rs12328637	0.97[ASN][1000 genomes]
rs12613282	0.81[ASN][1000 genomes]
rs12714199	0.82[ASN][1000 genomes]
rs12987172	0.81[ASN][1000 genomes]
rs12991654	0.82[ASN][1000 genomes]
rs13015620	0.81[ASN][1000 genomes]
rs1629293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs218059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs308902	0.85[EUR][1000 genomes]
rs308903	0.83[EUR][1000 genomes]
rs308910	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs308912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs308914	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs308915	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs308916	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs34666164	0.82[ASN][1000 genomes]
rs422240	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832042	0.81[ASN][1000 genomes]
rs4832045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4832300	0.81[ASN][1000 genomes]
rs4832302	0.82[ASN][1000 genomes]
rs4832303	0.81[ASN][1000 genomes]
rs4832304	0.96[ASN][1000 genomes]
rs62147239	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6733569	0.81[ASN][1000 genomes]
rs6750226	0.81[ASN][1000 genomes]
rs6752371	0.81[ASN][1000 genomes]
rs689912	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7570640	0.82[ASN][1000 genomes]
rs7584882	0.81[ASN][1000 genomes]
rs7587034	0.81[ASN][1000 genomes]
rs7601115	0.97[ASN][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
rs308900	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:86826800-86847800	Weak transcription	NHEK	skin
3	chr2:86828200-86847800	Weak transcription	NHLF	lung
4	chr2:86829400-86848400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:86829400-86849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:86829800-86849400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:86830000-86848600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:86830400-86847600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:86830400-86848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:86830800-86847600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:86830800-86847800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:86830800-86848000	Strong transcription	Placenta	Placenta
13	chr2:86831800-86848000	Weak transcription	HMEC	breast
14	chr2:86831800-86848200	Weak transcription	K562	blood
15	chr2:86832200-86848200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:86832400-86849400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:86832600-86848200	Weak transcription	Colonic Mucosa	Colon
18	chr2:86833000-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:86834600-86847400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:86834600-86847800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:86835200-86847800	Weak transcription	Hela-S3	cervix
22	chr2:86835800-86847600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:86836600-86848600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:86837000-86848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:86837200-86847800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:86839000-86847400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:86839400-86847400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:86839600-86847600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:86840200-86847400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr2:86840800-86847400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:86840800-86847600	Strong transcription	HSMM	muscle
32	chr2:86841000-86847600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:86841200-86847400	Weak transcription	Fetal Heart	heart
34	chr2:86841200-86847800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:86841200-86849600	Weak transcription	Gastric	stomach
36	chr2:86841200-86849600	Weak transcription	Spleen	Spleen
37	chr2:86841400-86849600	Weak transcription	Lung	lung
38	chr2:86841800-86847600	Strong transcription	Osteobl	bone
39	chr2:86842200-86847400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:86842200-86849600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:86843000-86848200	Weak transcription	Aorta	Aorta
42	chr2:86843000-86849600	Weak transcription	Esophagus	oesophagus
43	chr2:86843200-86847400	Genic enhancers	Brain Angular Gyrus	brain
44	chr2:86843200-86848000	Weak transcription	HSMMtube	muscle
45	chr2:86843200-86848200	Weak transcription	Psoas Muscle	Psoas
46	chr2:86843200-86849600	Weak transcription	Pancreas	Pancrea
47	chr2:86843400-86848200	Weak transcription	Thymus	Thymus
48	chr2:86843600-86847400	Enhancers	Brain Cingulate Gyrus	brain
49	chr2:86843600-86848000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:86844000-86847600	Genic enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links