Variant report

Variant	rs72698963
Chromosome Location	chr1:152416482-152416483
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11577946	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11579266	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12067942	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1923501	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2146117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36061814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56325026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696556	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72698953	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72698960	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72698964	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72698999	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv824664	chr1:152409024-152434443	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv463850	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv547858	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872445	chr1:152411813-152440753	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72698963	CRNN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152409800-152416600	Weak transcription	HSMM	muscle
2	chr1:152413800-152417000	Enhancers	Esophagus	oesophagus
3	chr1:152413800-152417000	Enhancers	Stomach Mucosa	stomach
4	chr1:152414800-152416800	Enhancers	HMEC	breast
5	chr1:152415200-152416600	Enhancers	Spleen	Spleen
6	chr1:152415400-152416800	Enhancers	HSMMtube	muscle
7	chr1:152415600-152416800	Enhancers	Brain Anterior Caudate	brain
8	chr1:152415600-152420000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:152415800-152416800	Enhancers	Lung	lung
10	chr1:152415800-152416800	Enhancers	Rectal Smooth Muscle	rectum
11	chr1:152415800-152417000	Enhancers	Brain Hippocampus Middle	brain
12	chr1:152415800-152417000	Enhancers	Brain Substantia Nigra	brain
13	chr1:152416000-152416800	Enhancers	Right Ventricle	heart
14	chr1:152416000-152417600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:152416200-152416800	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:152416400-152417000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr1:152416400-152420000	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:152416400-152423800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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