Variant report

Variant	rs3901856
Chromosome Location	chr6:118570514-118570515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10499086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1321985	0.88[ASN][1000 genomes]
rs1630266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1690658	0.88[ASN][1000 genomes]
rs1690664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1690667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17079881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17422275	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1743256	0.82[ASN][1000 genomes]
rs1743257	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1743258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1743259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1761620	0.88[ASN][1000 genomes]
rs1761622	0.88[ASN][1000 genomes]
rs1761624	0.82[ASN][1000 genomes]
rs1889468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3734345	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3851206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3900941	0.94[ASN][1000 genomes]
rs3904613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs62421485	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62421486	0.94[ASN][1000 genomes]
rs62421489	0.94[ASN][1000 genomes]
rs6924560	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7453860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9372498	0.94[ASN][1000 genomes]
rs937275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv428153	chr6:118430517-118586974	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1030089	chr6:118436482-118604516	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538427	chr6:118436482-118604516	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3901856	FAM26D	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118564800-118576400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:118570000-118570600	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:118570000-118571400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:118570000-118572200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:118570200-118570600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:118570200-118571200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:118570400-118570600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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