Variant report

Variant	rs2248899
Chromosome Location	chr10:54765036-54765037
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	chr10:54764008..54766836-chr10:54772750..54774326,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10824853	0.89[ASN][1000 genomes]
rs11003303	0.88[ASN][1000 genomes]
rs1343051	0.87[ASN][1000 genomes]
rs1343052	0.89[ASN][1000 genomes]
rs1343070	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1539512	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1880397	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917162	0.89[ASN][1000 genomes]
rs1917165	0.86[ASN][1000 genomes]
rs1917166	0.86[ASN][1000 genomes]
rs1917171	0.84[ASN][1000 genomes]
rs1935936	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1949816	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2066436	0.94[ASN][1000 genomes]
rs2140671	0.88[ASN][1000 genomes]
rs2244530	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2244637	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2244778	0.94[ASN][1000 genomes]
rs2249349	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249356	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253123	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2462480	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488606	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492355	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935055	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7095436	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2248899	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54757200-54766400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr10:54759800-54767200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr10:54760200-54765800	Weak transcription	Stomach Mucosa	stomach
4	chr10:54760800-54765600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:54761000-54766000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:54763400-54765400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr10:54763400-54765800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr10:54764400-54771200	Enhancers	HepG2	liver
9	chr10:54764600-54765200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:54764600-54765200	Enhancers	Fetal Thymus	thymus
11	chr10:54764600-54765600	Weak transcription	Fetal Intestine Small	intestine
12	chr10:54764600-54765600	Weak transcription	Fetal Kidney	kidney
13	chr10:54764800-54766000	Enhancers	GM12878-XiMat	blood
14	chr10:54764800-54767600	Enhancers	Liver	Liver
15	chr10:54765000-54765200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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