Variant report

Variant	rs9534987
Chromosome Location	chr13:48768609-48768610
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12100135	0.81[CHB][hapmap]
rs12870184	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12875750	0.81[CHB][hapmap]
rs12875956	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573601	0.81[CHB][hapmap]
rs2010173	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809328	0.81[CHB][hapmap]
rs520342	0.81[CHB][hapmap]
rs6561441	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561443	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320402	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333467	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316369	0.81[CHB][hapmap]
rs9526462	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534971	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534973	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534974	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534976	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534980	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534982	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534985	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534998	0.81[CHB][hapmap]
rs9535006	0.81[CHB][hapmap]
rs9535009	0.81[CHB][hapmap]
rs9562809	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562811	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568024	0.81[ASN][1000 genomes]
rs9568035	0.87[CHB][hapmap]
rs9634814	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3327569	chr13:48743550-48798094	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1043294	chr13:48762477-48810028	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv1031	chr13:48766510-48790172	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9534987	SERP2	cis	cerebellum	SCAN
rs9534987	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48764800-48774600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr13:48766400-48768800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr13:48766400-48769000	Enhancers	Primary T cells from cord blood	blood
4	chr13:48766400-48769000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr13:48766400-48769000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr13:48766400-48769000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr13:48766600-48769000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr13:48767000-48769600	Enhancers	Primary B cells from cord blood	blood
9	chr13:48767400-48769000	Enhancers	Primary hematopoietic stem cells	blood
10	chr13:48767400-48769000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr13:48767400-48769200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:48767400-48769400	Enhancers	Primary B cells from peripheral blood	blood
13	chr13:48767800-48768800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr13:48768000-48768800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:48768000-48768800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr13:48768000-48769000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr13:48768200-48769400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr13:48768400-48773000	Weak transcription	HepG2	liver
19	chr13:48768600-48769000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr13:48768600-48769000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:48768600-48769000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:48768600-48769600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr13:48768600-48773200	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links