Variant report

Variant	rs3958873
Chromosome Location	chr13:54874766-54874767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1334872	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409031	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3989423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338467	0.83[ASN][1000 genomes]
rs9536680	0.83[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	nsv471132	chr13:54788842-54885744	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54861800-54875400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:54869400-54879200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:54870600-54875400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:54873200-54875800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr13:54873200-54876200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr13:54873400-54874800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:54873600-54875400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr13:54874000-54875200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:54874400-54875200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:54874600-54875000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:54874600-54875800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr13:54874600-54876000	Genic enhancers	HUES6 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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