Variant report

Variant	rs12648731
Chromosome Location	chr4:158697324-158697325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10471081	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10857306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100133	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1904949	0.82[ASN][1000 genomes]
rs4273521	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4452481	1.00[ASN][1000 genomes]
rs6838375	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018387	chr4:157959931-158764190	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12648731	NPHP3	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158690400-158698400	Weak transcription	Fetal Intestine Large	intestine
2	chr4:158695800-158697600	Weak transcription	Fetal Intestine Small	intestine
3	chr4:158696800-158699200	Enhancers	Liver	Liver
4	chr4:158696800-158699200	Enhancers	HepG2	liver

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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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