Variant report

Variant	rs55947894
Chromosome Location	chr11:34805390-34805391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10047488	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11500298	0.82[AMR][1000 genomes]
rs11821869	0.90[EUR][1000 genomes]
rs12291335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16926116	0.93[EUR][1000 genomes]
rs16926295	0.82[AMR][1000 genomes]
rs2901525	0.82[AMR][1000 genomes]
rs3920862	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55774143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58208535	0.89[AFR][1000 genomes]
rs59115636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60196466	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60295827	0.89[AFR][1000 genomes]
rs60766133	0.89[AFR][1000 genomes]
rs60896094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124912	0.98[EUR][1000 genomes]
rs7483005	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978167	0.98[EUR][1000 genomes];1.00[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	nsv832117	chr11:34639008-34831199	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv869812	chr11:34648088-34810956	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv897214	chr11:34764251-34821948	Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs55947894	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs55947894	APIP	cis	Esophagus Mucosa	GTEx
rs55947894	APIP	cis	lung	GTEx
rs55947894	APIP	cis	Thyroid	GTEx
rs55947894	APIP	cis	Adipose Subcutaneous	GTEx
rs55947894	APIP	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34787600-34805600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:34792200-34811000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:34802800-34811200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:34804000-34811000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:34804800-34805800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr11:34804800-34806600	Flanking Active TSS	HepG2	liver
7	chr11:34805000-34806400	Enhancers	Stomach Mucosa	stomach
8	chr11:34805200-34805800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:34805200-34806000	Enhancers	K562	blood
10	chr11:34805200-34806200	Flanking Active TSS	Liver	Liver

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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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