Variant report

Variant	rs1606297
Chromosome Location	chr5:100566739-100566740
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10062560	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1113244	0.91[EUR][1000 genomes]
rs11505129	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505143	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35800297	0.81[ASN][1000 genomes]
rs4422508	0.91[EUR][1000 genomes]
rs66488844	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6862162	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7723879	0.91[EUR][1000 genomes]
rs7726058	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv462320	chr5:100247554-100775607	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv599176	chr5:100247554-100775607	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv882477	chr5:100362071-100577695	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv528811	chr5:100424081-101218087	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1032191	chr5:100455166-100852106	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv882478	chr5:100478431-100584654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv516292	chr5:100490972-100925684	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2758007	chr5:100507726-100760722	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2759360	chr5:100507726-100760722	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2757125	chr5:100542114-100656591	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv35075	chr5:100542852-100656532	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv2753053	chr5:100543101-100636101	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv13171	chr5:100551009-100649385	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv818365	chr5:100552450-100635105	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1606297	SLCO4C1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100565200-100566800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:100566400-100566800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr5:100566400-100566800	Enhancers	H9 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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