Variant report

Variant	rs2498723
Chromosome Location	chr9:25577555-25577556
allele	C/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:5)

rs_ID	r²[population]
rs1332166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1332167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1537267	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7847170	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7847225	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv466309	chr9:25157678-25683220	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv613889	chr9:25157678-25683220	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1018570	chr9:25170659-25633419	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv540100	chr9:25170659-25633419	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv869035	chr9:25287213-25779281	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1033677	chr9:25325400-25583227	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv540101	chr9:25325400-25583227	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv531597	chr9:25325401-25779422	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv613912	chr9:25538362-25722614	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv533233	chr9:25548163-25702906	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv613913	chr9:25548319-25621151	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892827	chr9:25551426-25603439	Enhancers Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv466316	chr9:25562454-25598674	Weak transcription Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
14	nsv466318	chr9:25562454-25598674	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
15	nsv613914	chr9:25562454-25598674	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv466319	chr9:25562454-25599995	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv613915	chr9:25562454-25599995	Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv831530	chr9:25563811-25754022	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2498723	PPP4R4	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25576200-25577600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:25577400-25578600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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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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