Variant report

Variant	rs4672072
Chromosome Location	chr2:56000565-56000566
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11678312	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679173	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367229	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17369365	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28789713	0.81[EUR][1000 genomes]
rs4671258	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704679	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797607	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797613	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72805666	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72805668	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72814246	0.86[AMR][1000 genomes];1.00[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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv999962	chr2:55976574-56011517	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv997683	chr2:55976574-56013875	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv431080	chr2:55988293-56011517	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672072	ZNF616	trans	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55989400-56015000	Weak transcription	Aorta	Aorta
2	chr2:55999800-56003000	Weak transcription	Stomach Mucosa	stomach
3	chr2:55999800-56003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:56000000-56001800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:56000000-56003400	Weak transcription	NHEK	skin
6	chr2:56000000-56003600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:56000000-56003600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:56000000-56003600	Weak transcription	HMEC	breast
9	chr2:56000000-56005000	Weak transcription	A549	lung
10	chr2:56000000-56005200	Weak transcription	Hela-S3	cervix
11	chr2:56000200-56002200	Weak transcription	HUVEC	blood vessel

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