Variant report

Variant	rs13395754
Chromosome Location	chr2:30664111-30664112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10180482	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10201729	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10202174	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12993078	0.81[ASN][1000 genomes]
rs13014119	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13017224	0.92[ASN][1000 genomes]
rs1357850	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1525063	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17038632	0.81[ASN][1000 genomes]
rs28666424	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35116667	0.95[ASN][1000 genomes]
rs36072623	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56150357	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62139608	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6705814	0.81[ASN][1000 genomes]
rs6724421	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6739322	0.81[ASN][1000 genomes]
rs894788	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13395754	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30658200-30665600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:30661600-30669400	Weak transcription	Primary B cells from cord blood	blood
3	chr2:30661800-30665400	Weak transcription	K562	blood
4	chr2:30663000-30669400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:30663200-30669400	Weak transcription	Thymus	Thymus
6	chr2:30663200-30669600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:30663600-30669000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:30663600-30669000	Weak transcription	Fetal Heart	heart
9	chr2:30663600-30669400	Weak transcription	Primary T cells from cord blood	blood
10	chr2:30663800-30669400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:30664000-30664200	Enhancers	H1 Cell Line	embryonic stem cell

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