Variant report

Variant	rs10458561
Chromosome Location	chr1:70921173-70921174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10889869	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10889871	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1145919	0.81[EUR][1000 genomes]
rs11590089	0.85[EUR][1000 genomes]
rs12029858	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1960400	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1967189	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650049	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4650051	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473334	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs577476	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs583316	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58977414	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663649	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs9633291	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv461828	chr1:70880717-70922360	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546456	chr1:70880717-70922360	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1002709	chr1:70916210-70939526	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Antipsychotic-induced QTc interval prolongation	20921969	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10458561	SRSF11	cis	cerebellum	SCAN
rs10458561	LRRIQ3	cis	parietal	SCAN
rs10458561	LRRC40	cis	cerebellum	SCAN
rs10458561	CTH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70909000-70928200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:70917200-70925600	Weak transcription	NHDF-Ad	bronchial
3	chr1:70921000-70921400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:70921000-70921600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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