Variant report

Variant	rs6680821
Chromosome Location	chr1:223856884-223856885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10799380	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10916022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916078	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[EUR][1000 genomes]
rs10916102	0.99[EUR][1000 genomes]
rs1109221	0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11587370	0.95[EUR][1000 genomes]
rs12733404	1.00[EUR][1000 genomes]
rs12758660	0.99[EUR][1000 genomes]
rs1573242	0.83[CHB][hapmap]
rs1936526	0.84[CHB][hapmap]
rs6668514	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs6692983	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs7522890	1.00[EUR][1000 genomes]
rs7525504	0.98[EUR][1000 genomes]
rs7540693	0.99[EUR][1000 genomes]
rs7547741	1.00[EUR][1000 genomes]
rs7556396	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6680821	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223851800-223857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:223853400-223857000	Enhancers	Stomach Mucosa	stomach
3	chr1:223853800-223857000	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:223853800-223858400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:223854800-223857000	Enhancers	Colonic Mucosa	Colon
6	chr1:223855000-223857000	Enhancers	Gastric	stomach
7	chr1:223855400-223859600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:223855800-223857000	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr1:223855800-223857400	Weak transcription	NHDF-Ad	bronchial
10	chr1:223855800-223865800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:223856000-223858200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:223856800-223858200	Weak transcription	HMEC	breast
13	chr1:223856800-223862200	Weak transcription	Pancreas	Pancrea

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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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