Variant report

Variant	rs7335107
Chromosome Location	chr13:54968613-54968614
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10870871	0.81[EUR][1000 genomes]
rs11148304	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs12858615	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591606	0.93[EUR][1000 genomes]
rs4517664	0.86[AFR][1000 genomes]
rs61954786	0.92[EUR][1000 genomes]
rs7322723	0.84[AFR][1000 genomes]
rs7328189	0.88[EUR][1000 genomes]
rs7331944	0.82[EUR][1000 genomes]
rs7336253	0.88[EUR][1000 genomes]
rs7489856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985620	0.82[AFR][1000 genomes]
rs9536717	0.81[AFR][1000 genomes]
rs9563221	0.91[JPT][hapmap]
rs9569023	0.91[EUR][1000 genomes]
rs9569029	0.91[EUR][1000 genomes]
rs9569033	0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.91[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7335107	NEK3	cis	parietal	SCAN
rs7335107	C13orf1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54967600-54970400	Enhancers	Fetal Intestine Large	intestine
2	chr13:54968000-54969600	Enhancers	Fetal Intestine Small	intestine
3	chr13:54968400-54969000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr13:54968400-54969200	Enhancers	Duodenum Mucosa	Duodenum
5	chr13:54968400-54969600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr13:54968400-54969600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr13:54968600-54968800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr13:54968600-54968800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr13:54968600-54969200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr13:54968600-54969400	Enhancers	HUES48 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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