Variant report

Variant	rs2961663
Chromosome Location	chr5:177613544-177613545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10073429	1.00[ASN][1000 genomes]
rs11743318	0.86[EUR][1000 genomes]
rs2913792	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913797	1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961665	0.87[YRI][hapmap]
rs2961671	0.81[TSI][hapmap]
rs7379857	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7380658	0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7715618	0.86[GIH][hapmap];1.00[ASN][1000 genomes]
rs7719717	0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9329136	0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9784730	0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv1017664	chr5:177578194-177633116	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
6	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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	106 gene(s)	inside rSNPs	diseases
7	nsv883193	chr5:177591495-177620189	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv883194	chr5:177604268-177620189	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv965585	chr5:177611416-177613608	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Rheumatoid arthritis	21156761	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2961663	BACE2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177609800-177614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:177609800-177621000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:177612600-177614200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr5:177612800-177613800	Enhancers	K562	blood
5	chr5:177613000-177613600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:177613000-177614400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:177613000-177614400	Enhancers	Primary hematopoietic stem cells	blood
8	chr5:177613200-177614000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:177613400-177613800	Weak transcription	Esophagus	oesophagus
10	chr5:177613400-177614400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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