Variant report

Variant	rs9568485
Chromosome Location	chr13:51461086-51461087
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs7316976	0.89[CHB][hapmap]
rs73186349	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73186350	0.86[EUR][1000 genomes]
rs73186351	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73186353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73186356	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73186357	0.89[AFR][1000 genomes]
rs9316510	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526702	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9563009	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568486	1.00[CEU][hapmap]
rs9568487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568488	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568489	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
2	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv900078	chr13:51454896-51478716	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv983515	chr13:51456419-51463427	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9568485	LCP1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51457200-51464600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr13:51458600-51461200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr13:51458800-51463400	Weak transcription	Fetal Thymus	thymus
4	chr13:51459200-51461200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr13:51459400-51461200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr13:51461000-51461800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr13:51461000-51462000	Enhancers	Primary hematopoietic stem cells	blood
8	chr13:51461000-51462000	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr13:51461000-51462200	Enhancers	Primary B cells from cord blood	blood
10	chr13:51461000-51462600	Weak transcription	Dnd41	blood

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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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