Variant report

Variant	rs9596952
Chromosome Location	chr13:54956487-54956488
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10047802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510486	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34883109	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35451065	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61954782	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61954783	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61954784	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6561776	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs73201621	0.96[ASN][1000 genomes]
rs73201626	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7322728	0.88[ASN][1000 genomes]
rs7335700	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8001623	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316714	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9591590	0.90[ASN][1000 genomes]
rs9591591	0.85[ASN][1000 genomes]
rs9591592	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs9596953	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9596954	0.87[ASN][1000 genomes]
rs9596955	0.90[ASN][1000 genomes]
rs9805180	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	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
2	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
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9596952	OLFM4	cis	cerebellum	SCAN
rs9596952	TRIM13	cis	parietal	SCAN
rs9596952	LECT1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54955600-54958000	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr13:54955800-54956600	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr13:54955800-54957800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr13:54955800-54958000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr13:54956000-54956600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr13:54956000-54958400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr13:54956000-54958400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr13:54956200-54957800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:54956400-54957600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:54956400-54957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links