Variant report

Variant	rs56000946
Chromosome Location	chr1:239577911-239577912
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55724527	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55978726	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56293463	1.00[AMR][1000 genomes]
rs57533762	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60564612	1.00[AMR][1000 genomes]
rs60707729	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61472058	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74149050	1.00[AMR][1000 genomes]
rs74149051	1.00[AMR][1000 genomes]
rs74149052	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74149053	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74149054	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74149059	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1006640	chr1:239290853-239658788	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535358	chr1:239290853-239658788	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873349	chr1:239475925-239587512	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873350	chr1:239498915-239648140	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239570600-239581400	Weak transcription	Ovary	ovary
2	chr1:239572800-239581400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:239576600-239585000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:239576800-239583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239576800-239586800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:239577000-239578600	Active TSS	Stomach Smooth Muscle	stomach
7	chr1:239577200-239578000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:239577200-239578400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:239577400-239578000	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:239577400-239578000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:239577400-239578000	Enhancers	Stomach Mucosa	stomach
12	chr1:239577600-239578000	Enhancers	Brain Germinal Matrix	brain
13	chr1:239577600-239580600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:239577800-239578000	Enhancers	Colon Smooth Muscle	Colon
15	chr1:239577800-239581400	Weak transcription	Fetal Brain Female	brain

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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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