Variant report

Variant	rs7336253
Chromosome Location	chr13:54947518-54947519
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10870871	0.80[EUR][1000 genomes]
rs11148304	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12429754	0.90[EUR][1000 genomes]
rs12858615	0.93[EUR][1000 genomes]
rs1336988	0.89[CEU][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs1591606	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2210930	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61954780	0.87[EUR][1000 genomes]
rs61954786	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7328189	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331944	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7335107	0.88[EUR][1000 genomes]
rs7489856	0.88[EUR][1000 genomes]
rs9563221	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9569023	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9569029	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9569033	0.89[CEU][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7336253	C13orf1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54942200-54948000	Weak transcription	Adipose Nuclei	Adipose
2	chr13:54946400-54947600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:54946400-54949600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr13:54947000-54949200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr13:54947000-54949200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:54947000-54949400	Enhancers	Fetal Brain Male	brain
7	chr13:54947200-54947600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr13:54947200-54947800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr13:54947200-54948200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:54947200-54948800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr13:54947200-54949000	Enhancers	Brain Germinal Matrix	brain
12	chr13:54947200-54949200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr13:54947200-54949200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr13:54947200-54949200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr13:54947200-54950600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr13:54947400-54948200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:54947400-54949000	Enhancers	Fetal Brain Female	brain
18	chr13:54947400-54949200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr13:54947400-54949600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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

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