Variant report

Variant	rs10878373
Chromosome Location	chr12:66465796-66465797
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11176028	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176057	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1168745	0.95[CEU][hapmap];1.00[GIH][hapmap]
rs1168754	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1732886	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs1732887	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1732888	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2701652	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2870784	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73123417	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952988	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953500	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966543	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966800	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7974467	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8793	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10878373	RP11-745O10.2	cis	Thyroid	GTEx
rs10878373	RP11-745O10.2	cis	Whole Blood	GTEx
rs10878373	IRAK3	Cis_1M	lymphoblastoid	RTeQTL
rs10878373	RP11-745O10.2	cis	Muscle Skeletal	GTEx
rs10878373	RP11-745O10.2	cis	lung	GTEx
rs10878373	RP11-745O10.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66460800-66466000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:66464600-66467000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:66464800-66466400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:66464800-66466800	Enhancers	Primary hematopoietic stem cells	blood
5	chr12:66464800-66466800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:66465000-66466000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:66465200-66466000	Enhancers	Primary B cells from cord blood	blood
8	chr12:66465200-66466800	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:66465200-66466800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:66465400-66466600	Flanking Active TSS	GM12878-XiMat	blood

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links