Variant report

Variant	rs566091
Chromosome Location	chr4:152852168-152852169
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr4:152851423-152852211	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000249818	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1631928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165575	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs184867	0.81[AFR][1000 genomes]
rs189672	0.81[GIH][hapmap]
rs2113977	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs244403	0.81[AFR][1000 genomes]
rs360919	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs360920	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs360938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs361110	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs361133	0.83[CEU][hapmap]
rs361140	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs361159	1.00[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs361160	1.00[CEU][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs471230	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs509848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518055	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs523646	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs551375	0.86[EUR][1000 genomes]
rs692907	0.81[EUR][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	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
2	nsv1030328	chr4:152791533-152875666	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1028836	chr4:152791680-152879097	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs566091	TMEM154	cis	parietal	SCAN
rs566091	FGG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152851400-152852200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:152851400-152852200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr4:152851400-152852200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:152851600-152852200	Enhancers	Brain Germinal Matrix	brain
5	chr4:152851800-152852200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:152851800-152852200	Enhancers	Fetal Heart	heart
7	chr4:152852000-152854200	Weak transcription	Fetal Thymus	thymus

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