Variant report

Variant	rs2490162
Chromosome Location	chr6:48796193-48796194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12205761	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938176	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938179	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938184	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938190	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1938191	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2096425	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2186212	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7760095	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7760648	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7768096	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367335	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9369820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9381702	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9381703	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395415	0.91[EUR][1000 genomes];0.88[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	nsv1033151	chr6:48067287-48797029	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv538217	chr6:48067287-48797029	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv949690	chr6:48595821-49289855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2490162	CRISP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:48794200-48797000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:48794600-48796600	Enhancers	HMEC	breast
3	chr6:48795000-48797000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:48795200-48796200	Enhancers	A549	lung
5	chr6:48795200-48796400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:48795200-48797000	Enhancers	Stomach Mucosa	stomach
7	chr6:48795200-48797200	Enhancers	NHEK	skin
8	chr6:48795400-48796400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:48795600-48796400	Enhancers	NHLF	lung
10	chr6:48795600-48796400	Weak transcription	Osteobl	bone
11	chr6:48795600-48797400	Enhancers	Hela-S3	cervix
12	chr6:48795800-48796200	Weak transcription	NHDF-Ad	bronchial
13	chr6:48795800-48796400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:48795800-48796600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:48796000-48796200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr6:48796000-48797000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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