Variant report

Variant	rs5028355
Chromosome Location	chr11:76953939-76953940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10899366	0.82[YRI][hapmap]
rs10899367	0.85[YRI][hapmap]
rs12271408	0.81[ASN][1000 genomes]
rs2156566	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2729758	0.82[YRI][hapmap]
rs2729772	0.82[YRI][hapmap]
rs3740769	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3901607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4281503	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944150	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4945164	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7125798	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7935940	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs954924	0.88[EUR][1000 genomes];0.98[ASN][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	nsv534515	chr11:76900813-77035769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5028355	RPS3	cis	cerebellum	SCAN
rs5028355	DNAJB13	cis	parietal	SCAN
rs5028355	P2RY2	cis	parietal	SCAN
rs5028355	MRPL48	cis	parietal	SCAN
rs5028355	C2CD3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76944600-76954600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:76949000-76954800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:76949200-76954600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:76953400-76954600	Enhancers	HepG2	liver
5	chr11:76953800-76955200	Enhancers	Fetal Intestine Large	intestine
6	chr11:76953800-76956000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:76953800-76956200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr11:76953800-76956400	Enhancers	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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