Variant report

Variant	rs534861
Chromosome Location	chr17:15690793-15690794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10852832	0.82[ASN][1000 genomes]
rs1596353	0.81[ASN][1000 genomes]
rs533073	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
4	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv907705	chr17:15611495-15717546	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
8	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
9	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv442411	chr17:15677001-15694785	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	6 gene(s)	inside rSNPs	diseases
11	esv3406800	chr17:15688452-15691000	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	esv3342426	chr17:15688677-15690975	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs534861	CTD-3157E16.1	cis	Nerve Tibial	GTEx
rs534861	CTD-3157E16.1	cis	lung	GTEx
rs534861	CTD-3157E16.1	cis	Thyroid	GTEx
rs534861	CTD-3157E16.1	cis	Esophagus Muscularis	GTEx
rs534861	CTD-3157E16.1	cis	Artery Aorta	GTEx
rs534861	CTD-3157E16.1	cis	Adipose Subcutaneous	GTEx
rs534861	CTD-3157E16.1	cis	Artery Tibial	GTEx
rs534861	MEIS3P1	cis	Artery Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15686600-15691400	Weak transcription	Gastric	stomach
2	chr17:15689800-15690800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:15690000-15691800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:15690000-15691800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr17:15690200-15690800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:15690200-15690800	Weak transcription	Fetal Intestine Small	intestine
7	chr17:15690200-15691800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr17:15690200-15692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:15690200-15692000	Weak transcription	Fetal Stomach	stomach
10	chr17:15690200-15692200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr17:15690200-15692800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:15690200-15692800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:15690200-15693000	Weak transcription	Right Ventricle	heart
14	chr17:15690400-15691200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:15690400-15691800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr17:15690400-15692000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:15690600-15691400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

Quick Search:

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

what's new

Quick links