Variant report

Variant	rs6693360
Chromosome Location	chr1:224808949-224808950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10799588	0.88[ASN][1000 genomes]
rs11802812	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11803050	1.00[AMR][1000 genomes]
rs11804994	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs16849654	1.00[JPT][hapmap]
rs57209437	0.93[ASN][1000 genomes]
rs58565730	0.93[ASN][1000 genomes]
rs59018094	0.80[ASN][1000 genomes]
rs59610983	0.93[ASN][1000 genomes]
rs59643307	0.93[ASN][1000 genomes]
rs61247305	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6657458	0.93[ASN][1000 genomes]
rs7534595	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7539939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7550112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6693360	CAPN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224805800-224812200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:224806000-224811800	Weak transcription	Spleen	Spleen
3	chr1:224806200-224810400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:224806200-224810400	Weak transcription	Pancreas	Pancrea
5	chr1:224806600-224812800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:224806600-224813600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:224807000-224809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:224807000-224810600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:224807400-224809800	Weak transcription	HMEC	breast
10	chr1:224808000-224810200	Weak transcription	NHLF	lung
11	chr1:224808200-224809200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:224808200-224809400	Enhancers	NH-A	brain
13	chr1:224808800-224809600	ZNF genes & repeats	NHDF-Ad	bronchial
14	chr1:224808800-224810000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:224808800-224810200	Genic enhancers	Dnd41	blood
16	chr1:224808800-224812400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

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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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