Variant report

Variant	rs6588397
Chromosome Location	chr1:47943032-47943033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11211540	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11211542	0.82[EUR][1000 genomes]
rs11800497	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12025418	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12057975	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12073605	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1337524	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4926556	0.85[EUR][1000 genomes]
rs6668106	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6675690	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7520501	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7537074	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7539808	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[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	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv2755190	chr1:47907580-48048680	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47934400-47950600	Weak transcription	Right Atrium	heart
2	chr1:47935000-47943400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:47935000-47943600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47935000-47943600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:47936000-47945400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:47940000-47943400	Enhancers	Stomach Mucosa	stomach
7	chr1:47942000-47946800	Enhancers	Liver	Liver
8	chr1:47942400-47944800	Enhancers	Gastric	stomach
9	chr1:47942800-47943600	Enhancers	Colonic Mucosa	Colon
10	chr1:47942800-47943600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:47942800-47944600	Enhancers	Fetal Intestine Small	intestine
12	chr1:47943000-47943200	Enhancers	Fetal Kidney	kidney
13	chr1:47943000-47943800	Flanking Active TSS	A549	lung
14	chr1:47943000-47944200	Enhancers	Small Intestine	intestine
15	chr1:47943000-47944400	Enhancers	Adipose Nuclei	Adipose
16	chr1:47943000-47944400	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:47943000-47944400	Enhancers	HepG2	liver
18	chr1:47943000-47944600	Enhancers	Fetal Intestine Large	intestine
19	chr1:47943000-47944600	Enhancers	Sigmoid Colon	Sigmoid Colon

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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