Variant report

Variant	rs12125889
Chromosome Location	chr1:75241971-75241972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10161	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12129513	0.81[CEU][hapmap];0.94[AMR][1000 genomes]
rs1574941	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1590639	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17618340	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345438	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28535522	0.95[AMR][1000 genomes]
rs28594379	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28640981	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28804435	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35497701	0.93[AMR][1000 genomes]
rs3845356	0.82[YRI][hapmap]
rs3889133	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55895041	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6668736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.82[YRI][hapmap]

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	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv871743	chr1:75235082-75714554	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12125889	CRYZ	cis	cerebellum	SCAN
rs12125889	CRYZ	cis	Adipose Subcutaneous	GTEx
rs12125889	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs12125889	CRYZ	cis	Nerve Tibial	GTEx
rs12125889	CRYZ	cis	parietal	SCAN
rs12125889	TYW3	cis	cerebellum	SCAN
rs12125889	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs12125889	CRYZ	cis	lesional skin	skin_eQTL
rs12125889	CRYZ	cis	lymphoblastoid	seeQTL
rs12125889	CRYZ	cis	uninvolved skin	skin_eQTL
rs12125889	CRYZ	cis	multi-tissue	Pritchard
rs12125889	TYW3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75231200-75245600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:75231200-75246000	Weak transcription	iPS-20b 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