Variant report

Variant	rs12408790
Chromosome Location	chr1:76502895-76502896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11579206	0.80[AMR][1000 genomes]
rs12405897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12411016	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251482	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251483	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1251522	0.87[AMR][1000 genomes]
rs1658741	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17657999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1770896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1892480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2004130	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4949620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4949689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72988522	1.00[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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2754129	chr1:76489579-76529279	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76492600-76503400	Weak transcription	Fetal Lung	lung
2	chr1:76500200-76503000	Weak transcription	Fetal Kidney	kidney
3	chr1:76501600-76503400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:76501800-76503400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:76501800-76503600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:76501800-76504200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:76501800-76504400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:76502000-76503600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:76502200-76507200	Enhancers	Fetal Intestine Large	intestine
10	chr1:76502200-76507400	Enhancers	Fetal Intestine Small	intestine
11	chr1:76502600-76503000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:76502600-76503000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:76502600-76503800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:76502800-76503200	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr1:76502800-76503600	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:76502800-76504000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:76502800-76504200	Enhancers	Stomach Mucosa	stomach

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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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