Variant report

Variant	rs3893377
Chromosome Location	chr4:15742129-15742130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10000290	0.84[ASN][1000 genomes]
rs10019008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023845	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10222984	0.82[EUR][1000 genomes]
rs11933202	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11947310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286880	0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs28608142	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893376	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs73224677	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998153	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Current cigarettes per day in chronic obstructive pulmonary disease	21685187	GWAS catalog

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15707400-15742800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:15723000-15743000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:15723000-15744600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:15729000-15743200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:15733600-15742800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:15735400-15742800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:15738400-15742600	Enhancers	Dnd41	blood
8	chr4:15740800-15742200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:15741400-15743600	Enhancers	Liver	Liver
10	chr4:15741800-15743200	Enhancers	HepG2	liver
11	chr4:15742000-15742600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:15742000-15742600	Enhancers	Adipose Nuclei	Adipose

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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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