Variant report

Variant	rs28551643
Chromosome Location	chr15:78232972-78232973
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11638281	0.83[EUR][1000 genomes]
rs12899446	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17476095	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4563013	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886977	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv904426	chr15:78090630-78264164	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904427	chr15:78129964-78251431	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv976954	chr15:78153346-78255825	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv904429	chr15:78160362-78251431	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28551643	RP11-114H24.2	cis	Esophagus Muscularis	GTEx
rs28551643	RP11-114H24.2	cis	Muscle Skeletal	GTEx
rs28551643	RP11-114H24.2	cis	Nerve Tibial	GTEx
rs28551643	RP11-114H24.2	cis	lung	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78226800-78236200	Weak transcription	Spleen	Spleen
2	chr15:78231400-78233000	Enhancers	HepG2	liver
3	chr15:78231400-78236400	Weak transcription	Placenta	Placenta
4	chr15:78231600-78236400	Weak transcription	HSMM	muscle
5	chr15:78231800-78234400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:78231800-78236200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:78231800-78236400	Weak transcription	Fetal Lung	lung
8	chr15:78232200-78233000	Enhancers	Esophagus	oesophagus
9	chr15:78232200-78233000	Enhancers	Fetal Intestine Large	intestine
10	chr15:78232200-78233000	Enhancers	Fetal Intestine Small	intestine
11	chr15:78232200-78236400	Weak transcription	HSMMtube	muscle
12	chr15:78232800-78233000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
13	chr15:78232800-78233000	Enhancers	Fetal Muscle Leg	muscle
14	chr15:78232800-78233000	Enhancers	Fetal Stomach	stomach
15	chr15:78232800-78236200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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