Variant report

Variant	rs11858408
Chromosome Location	chr15:34508905-34508906
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:34393498..34396367-chr15:34507556..34509302,2	K562	blood:
2	chr15:34402294..34404744-chr15:34506028..34509076,3	MCF-7	breast:
3	chr15:34507802..34510107-chr15:34514805..34516996,3	K562	blood:
4	chr15:34501162..34503390-chr15:34507546..34510733,3	K562	blood:
5	chr15:34499403..34506943-chr15:34508287..34513350,9	K562	blood:
6	chr15:34507877..34510107-chr15:34514805..34516525,2	K562	blood:
7	chr15:34499153..34500903-chr15:34508468..34510016,2	K562	blood:

Variant related genes	Relation type
ENSG00000134152	Chromatin interaction
ENSG00000134153	Chromatin interaction
ENSG00000182405	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10851952	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10851955	0.96[ASN][1000 genomes]
rs11073010	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11073014	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11073019	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631981	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11635964	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11854686	0.85[ASN][1000 genomes]
rs11857205	0.85[ASN][1000 genomes]
rs12437551	0.92[ASN][1000 genomes]
rs12441003	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442758	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591315	0.87[EUR][1000 genomes]
rs12917397	0.92[ASN][1000 genomes]
rs1978810	0.85[ASN][1000 genomes]
rs28652966	0.90[ASN][1000 genomes]
rs4381574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780227	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4780229	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4780232	0.83[EUR][1000 genomes]
rs56731918	0.88[ASN][1000 genomes]
rs57502425	0.86[ASN][1000 genomes]
rs58875083	0.88[ASN][1000 genomes]
rs6495619	0.81[ASN][1000 genomes]
rs6495621	0.83[ASN][1000 genomes]
rs6495625	0.85[ASN][1000 genomes]
rs7164448	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7168619	0.82[ASN][1000 genomes]
rs7168761	0.82[ASN][1000 genomes]
rs7174014	0.81[ASN][1000 genomes]
rs7178988	0.88[ASN][1000 genomes]
rs7180200	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7181687	0.88[ASN][1000 genomes]
rs7181902	0.88[ASN][1000 genomes]
rs8026939	0.90[ASN][1000 genomes]
rs8027499	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027830	0.88[ASN][1000 genomes]
rs8028027	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8034315	0.88[ASN][1000 genomes]
rs8036468	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8040071	0.85[ASN][1000 genomes]
rs8041586	0.83[ASN][1000 genomes]
rs8041977	0.86[ASN][1000 genomes]
rs8043216	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9972505	0.88[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	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11858408	NOP10	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34502600-34510000	Weak transcription	NHLF	lung
2	chr15:34505000-34510200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:34507000-34509600	Weak transcription	K562	blood
4	chr15:34507200-34516200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:34508400-34509200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:34508400-34509200	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links