Variant report

Variant	rs2496368
Chromosome Location	chr6:49111495-49111496
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10948484	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2496356	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2516121	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516123	0.90[ASN][1000 genomes]
rs4510676	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6927013	0.86[CHB][hapmap]
rs6938215	0.88[ASN][1000 genomes]
rs7776038	0.85[ASN][1000 genomes]
rs9367347	0.88[ASN][1000 genomes]
rs9369860	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[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	nsv949690	chr6:48595821-49289855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv603049	chr6:48931959-49169337	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2755862	chr6:49081541-49298041	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2496368	CENPQ	cis	Artery Tibial	GTEx
rs2496368	CENPQ	cis	Esophagus Muscularis	GTEx
rs2496368	CENPQ	cis	Adipose Subcutaneous	GTEx
rs2496368	MUT	cis	Nerve Tibial	GTEx
rs2496368	CENPQ	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49108400-49111800	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr6:49108600-49112000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:49108800-49111600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr6:49109000-49112000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr6:49109600-49112200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:49110600-49111800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:49111000-49112000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr6:49111000-49112000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:49111200-49111800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:49111400-49111800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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