Variant report

Variant	rs16878852
Chromosome Location	chr4:27115685-27115686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16878830	0.80[EUR][1000 genomes]
rs16878849	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878854	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17572822	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56077414	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56105534	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56159027	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58071741	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73251795	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73251799	0.80[EUR][1000 genomes]
rs73251800	0.84[EUR][1000 genomes]
rs73251801	0.84[EUR][1000 genomes]
rs73251802	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73253660	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73253664	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73253667	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73253668	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002082	chr4:27078850-27377252	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv997608	chr4:27085524-27371848	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv999134	chr4:27115301-27270500	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16878852	ANKRD28	trans	brain	seeQTL
rs16878852	PDZK1	trans	brain	seeQTL
rs16878852	FAT2	trans	brain	seeQTL
rs16878852	CRTAM	trans	brain	seeQTL
rs16878852	SCGN	trans	brain	seeQTL
rs16878852	SOD3	cis	cerebellum	SCAN
rs16878852	AMICA1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:27111600-27117000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:27114000-27116200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:27114000-27116600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:27114600-27116200	Weak transcription	ES-UCSF4 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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