Variant report

Variant	rs11746901
Chromosome Location	chr5:59781702-59781703
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10045433	0.81[CEU][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap]
rs10471256	0.81[CEU][hapmap]
rs10939840	1.00[CHD][hapmap]
rs10939842	1.00[CHD][hapmap]
rs10939849	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11740770	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11948687	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12153271	1.00[CHD][hapmap]
rs12153798	0.94[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12188950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16877912	1.00[CHD][hapmap]
rs16878144	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28481826	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2898278	0.82[CEU][hapmap]
rs6449470	1.00[CHD][hapmap]
rs6868537	0.81[CEU][hapmap]
rs73108664	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7719095	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11746901	PDE4D	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59741800-59783200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:59767200-59789000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:59779200-59783000	Weak transcription	HMEC	breast
4	chr5:59779200-59783400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:59779200-59783400	Weak transcription	NHEK	skin
6	chr5:59779400-59782400	Weak transcription	A549	lung
7	chr5:59779400-59783200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:59779800-59782200	Enhancers	HepG2	liver
9	chr5:59779800-59783000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:59780000-59783400	Weak transcription	HSMM	muscle
11	chr5:59780600-59782000	Enhancers	Fetal Brain Male	brain
12	chr5:59781400-59782000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:59781400-59786600	Active TSS	Aorta	Aorta
14	chr5:59781600-59782400	Weak transcription	Placenta Amnion	Placenta Amnion

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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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