Variant report

Variant	rs17554993
Chromosome Location	chr14:38438256-38438257
allele	C/T
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	FOS	chr14:38438143-38438343	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr14:38438130-38438298	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr14:38438066-38438350	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr14:38438082-38438348	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr14:38438026-38438330	MCF-7	breast:	n/a	chr14:38438223-38438236 chr14:38438289-38438302 chr14:38438224-38438235 chr14:38438223-38438236
6	CEBPB	chr14:38438127-38438385	HepG2	liver:	n/a	chr14:38438223-38438236 chr14:38438289-38438302 chr14:38438224-38438235 chr14:38438223-38438236
7	CEBPB	chr14:38438069-38438416	Hela-S3	cervix:	n/a	chr14:38438223-38438236 chr14:38438289-38438302 chr14:38438224-38438235 chr14:38438223-38438236

Variant related genes	Relation type
TTC6	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10134624	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10140719	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10145136	1.00[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs10145337	0.88[EUR][1000 genomes]
rs10146385	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10220355	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10483495	0.89[CEU][hapmap]
rs10872905	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1113092	1.00[CEU][hapmap]
rs11156973	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11156974	1.00[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs11621735	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs11622986	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1170022	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap]
rs1170023	0.92[CEU][hapmap]
rs1170024	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1170025	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1170028	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1170029	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1170030	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1170031	0.89[CEU][hapmap]
rs11851837	0.96[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12147106	0.84[CHB][hapmap]
rs12432452	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs12435640	0.96[CEU][hapmap]
rs12590816	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12882516	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs12883466	0.86[CHB][hapmap]
rs17107343	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs17179919	0.96[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs1952787	0.96[CEU][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1952788	0.96[CEU][hapmap]
rs1952789	0.86[CHB][hapmap]
rs1952790	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs1958692	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs1958693	1.00[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1958694	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1959676	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs2150322	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2183531	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2415421	0.87[EUR][1000 genomes]
rs2415422	0.85[EUR][1000 genomes]
rs35272292	0.83[EUR][1000 genomes]
rs3809444	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4143919	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4322573	0.93[CEU][hapmap]
rs4597229	0.92[CEU][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes]
rs4898785	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs4901412	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4901413	0.84[EUR][1000 genomes]
rs4901421	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4901422	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs4901423	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6571829	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs6571830	0.96[CEU][hapmap]
rs71407745	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71407747	0.86[EUR][1000 genomes]
rs7148370	0.90[EUR][1000 genomes]
rs7153182	0.90[EUR][1000 genomes]
rs7154853	0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs7155891	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs7158383	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8005651	1.00[CEU][hapmap]
rs8005895	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs8013747	0.96[CEU][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes]
rs8014896	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8015738	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs8020796	0.81[EUR][1000 genomes]
rs9322983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs954881	1.00[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs9788473	0.96[CEU][hapmap]
rs9788476	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv564387	chr14:38357864-38563111	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3365884	chr14:38419250-38438768	Weak transcription Enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv901651	chr14:38419360-38556242	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17554993	C14orf19	cis	cerebellum	SCAN
rs17554993	C14orf147	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38437400-38440600	Enhancers	Fetal Intestine Large	intestine
2	chr14:38437400-38440600	Enhancers	Stomach Mucosa	stomach
3	chr14:38437600-38439800	Enhancers	Dnd41	blood
4	chr14:38437800-38438600	Weak transcription	Pancreas	Pancrea
5	chr14:38438000-38438400	Weak transcription	Fetal Intestine Small	intestine
6	chr14:38438200-38438800	Enhancers	Pancreatic Islets	Pancreatic Islet

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