Variant report

Variant	rs1397684
Chromosome Location	chr4:152752413-152752414
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11943626	0.95[ASN][1000 genomes]
rs13109601	0.87[ASN][1000 genomes]
rs13136369	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2136960	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34359168	0.95[ASN][1000 genomes]
rs34615528	0.95[ASN][1000 genomes]
rs4279186	0.95[ASN][1000 genomes]
rs4337716	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4525955	0.95[ASN][1000 genomes]
rs56175637	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836954	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1397684	FAM160A1	cis	parietal	SCAN
rs1397684	SH3D19	cis	cerebellum	SCAN
rs1397684	PET112L	cis	parietal	SCAN
rs1397684	FAM160A1	cis	cerebellum	SCAN
rs1397684	PET112L	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152750200-152753400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:152751000-152752800	Enhancers	Brain Germinal Matrix	brain
3	chr4:152752000-152753000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:152752000-152753200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr4:152752000-152753400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:152752000-152753400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:152752000-152753400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr4:152752000-152754000	Weak transcription	GM12878-XiMat	blood
9	chr4:152752200-152755000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr4:152752400-152753200	Enhancers	HUES48 Cell Line	embryonic stem cell

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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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