Variant report

Variant	rs17276680
Chromosome Location	chr4:153099920-153099921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13107216	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13112628	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276701	0.86[CHD][hapmap]
rs17361412	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2001705	0.85[EUR][1000 genomes]
rs34174274	0.92[EUR][1000 genomes]
rs35225072	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35985138	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586908	0.85[EUR][1000 genomes]
rs62319036	0.86[AFR][1000 genomes];0.91[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	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv880774	chr4:153035743-153121818	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17276680	DCLK2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153097000-153109000	Weak transcription	Right Atrium	heart
2	chr4:153099000-153100400	Enhancers	Fetal Thymus	thymus
3	chr4:153099200-153100000	Enhancers	Primary T cells from cord blood	blood
4	chr4:153099200-153100000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr4:153099400-153100000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr4:153099600-153100000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:153099600-153100000	Enhancers	Thymus	Thymus

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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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