Variant report

Variant	rs3747556
Chromosome Location	chr12:41967677-41967678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10506198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1495778	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17121156	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17129486	0.91[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs17129547	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2007974	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4265646	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55724233	0.87[ASN][1000 genomes]
rs7133757	0.91[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs73115867	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73115875	0.95[EUR][1000 genomes]
rs73115879	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73115897	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73282231	0.87[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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3747556	USP13	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41959400-41970800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:41961400-41968600	Weak transcription	Fetal Brain Female	brain
3	chr12:41965000-41968400	Strong transcription	Stomach Smooth Muscle	stomach
4	chr12:41965800-41968200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:41965800-41968600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:41966200-41973000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:41966600-41973000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:41967000-41975600	Weak transcription	Aorta	Aorta
9	chr12:41967200-41972800	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:41967400-41976600	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:41967600-41972400	Weak transcription	Fetal Stomach	stomach
12	chr12:41967600-41973200	Weak transcription	Brain Germinal Matrix	brain

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