Variant report

Variant	rs6688859
Chromosome Location	chr1:113775761-113775762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12129081	0.88[EUR][1000 genomes]
rs12135259	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12138560	0.82[EUR][1000 genomes]
rs12146020	0.82[EUR][1000 genomes]
rs12730687	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6698871	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv2465	chr1:113731589-113776605	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv520749	chr1:113772733-113781358	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6688859	PHTF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113761000-113790200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:113774600-113775800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr1:113774800-113775800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:113774800-113776000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:113774800-113776800	Weak transcription	Fetal Intestine Small	intestine
6	chr1:113775000-113779200	Weak transcription	Fetal Intestine Large	intestine
7	chr1:113775200-113782600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:113775400-113775800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:113775400-113776800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:113775600-113776800	Weak transcription	H1 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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