Variant report

Variant	rs11576904
Chromosome Location	chr1:166878464-166878465
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	USF1	chr1:166878175-166878546	K562	blood:	n/a	n/a
2	FOS	chr1:166878235-166878548	MCF10A-Er-Src	breast:	n/a	n/a
3	BHLHE40	chr1:166878313-166878492	K562	blood:	n/a	n/a
4	FOS	chr1:166878209-166878531	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:166878207-166878571	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000237096	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10918599	0.90[ASN][1000 genomes]
rs10918600	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10918603	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11579987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11583927	0.88[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs11588176	0.89[ASN][1000 genomes]
rs1543313	0.90[EUR][1000 genomes]
rs2038020	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072740	0.87[EUR][1000 genomes]
rs2072742	0.83[ASN][1000 genomes]
rs2142615	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2223221	0.94[EUR][1000 genomes]
rs2235184	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2294220	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34381372	0.88[EUR][1000 genomes]
rs4656516	0.88[EUR][1000 genomes]
rs4657612	0.94[EUR][1000 genomes]
rs61815130	0.92[ASN][1000 genomes]
rs61815132	0.87[ASN][1000 genomes]
rs6427047	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6427048	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6677644	0.80[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs742048	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7513457	0.94[EUR][1000 genomes]
rs7520897	0.80[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs7545806	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9633326	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11576904	TBX19	cis	cerebellum	SCAN
rs11576904	APOA2	cis	cerebellum	SCAN
rs11576904	TADA1	cis	cerebellum	SCAN
rs11576904	MAEL	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166875600-166880000	Weak transcription	NHEK	skin
2	chr1:166875800-166878800	Enhancers	Placenta	Placenta
3	chr1:166875800-166880000	Weak transcription	HMEC	breast
4	chr1:166876400-166889400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:166876800-166889400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:166877200-166878600	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:166877200-166883200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:166877600-166880200	Weak transcription	GM12878-XiMat	blood
9	chr1:166877600-166880400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:166877800-166880200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:166877800-166880200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:166878400-166878600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:166878400-166878600	Bivalent Enhancer	HSMM	muscle
14	chr1:166878400-166878600	Bivalent Enhancer	HSMMtube	muscle
15	chr1:166878400-166880400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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