Variant report

Variant	rs2680672
Chromosome Location	chr3:53715973-53715974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12486415	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12492502	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12493744	0.82[CHB][hapmap]
rs1872999	0.99[ASN][1000 genomes]
rs1906537	0.88[ASN][1000 genomes]
rs2680658	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs34078083	0.96[ASN][1000 genomes]
rs62251938	0.84[ASN][1000 genomes]
rs6762231	0.87[CHB][hapmap]
rs6765728	0.96[ASN][1000 genomes]
rs6793312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6806330	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs735652	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7648561	0.94[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2680672	NEK4	cis	parietal	SCAN
rs2680672	RAD54L2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53713200-53716000	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53713800-53717600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:53714400-53722200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:53714600-53716800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:53714800-53717200	Strong transcription	Fetal Lung	lung
7	chr3:53715400-53716000	Enhancers	Psoas Muscle	Psoas
8	chr3:53715600-53739600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:53715800-53716400	Weak transcription	Fetal Intestine Small	intestine

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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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