Variant report

Variant	rs9569016
Chromosome Location	chr13:54901829-54901830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12583110	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12584722	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36101238	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4351942	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4359326	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4441145	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4592544	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4884962	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4884964	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7328868	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7331635	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7993684	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7994809	0.92[ASN][1000 genomes]
rs9316712	0.96[ASN][1000 genomes]
rs9527191	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536678	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9536679	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536681	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536682	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563209	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563210	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9563211	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563212	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9569014	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9569015	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9591581	0.87[ASN][1000 genomes]

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	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1051063	chr13:54777487-54997866	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv541778	chr13:54777487-54997866	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	esv3349795	chr13:54892694-55252030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9569016	SIX1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54880000-54929800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:54892600-54903800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr13:54892800-54923000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:54896600-54903000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr13:54898200-54902800	Weak transcription	Fetal Heart	heart
6	chr13:54898200-54903400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr13:54898400-54903000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr13:54898600-54905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:54901200-54903000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr13:54901400-54902000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:54901600-54902400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:54901600-54902800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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