Variant report

Variant	rs11857380
Chromosome Location	chr15:58712203-58712204
allele	G/T
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:15)

rs_ID	r²[population]
rs11854624	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856159	1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs11858279	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12440032	1.00[CHB][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs12440217	0.85[ASN][1000 genomes]
rs13329672	0.83[CHB][hapmap]
rs17240869	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17240876	0.84[ASN][1000 genomes]
rs17821310	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17821322	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs487766	0.90[CHB][hapmap]
rs55696635	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55993842	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62000868	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs62000870	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58694800-58716000	Weak transcription	Esophagus	oesophagus
2	chr15:58703000-58712800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:58703400-58718600	Weak transcription	Primary T cells from cord blood	blood
4	chr15:58704600-58728800	Weak transcription	Thymus	Thymus
5	chr15:58711000-58712400	Enhancers	GM12878-XiMat	blood
6	chr15:58711400-58716200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:58711600-58712400	Weak transcription	Placenta	Placenta
8	chr15:58711800-58722000	Enhancers	Liver	Liver
9	chr15:58712200-58712400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:58712200-58712600	Flanking Active TSS	HepG2	liver
11	chr15:58712200-58713000	Enhancers	K562	blood
12	chr15:58712200-58713800	Enhancers	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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