Variant report

Variant	rs4854241
Chromosome Location	chr2:95659249-95659250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95656114..95658110-chr2:95658278..95660478,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235186	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10172167	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[YRI][hapmap]
rs1875402	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs2291991	0.83[EUR][1000 genomes]
rs2320620	0.84[CEU][hapmap]
rs3105098	0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3105099	0.85[GIH][hapmap]
rs3105101	0.85[CEU][hapmap]
rs3105104	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs3105105	0.80[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs3112225	0.85[CEU][hapmap]
rs3112228	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs3112229	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs3112230	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs3112982	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3112983	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs3112984	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3112985	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs3112986	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3112987	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3112995	0.85[CEU][hapmap]
rs3112996	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs3112997	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs3113002	0.81[CHB][hapmap];0.85[GIH][hapmap]
rs4241315	0.90[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4555374	0.87[ASW][hapmap];0.95[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap]
rs4564804	0.87[ASW][hapmap];0.95[CEU][hapmap];0.81[TSI][hapmap]
rs4854243	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6708474	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs7565772	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582368	0.90[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7585473	0.81[AMR][1000 genomes]
rs872580	0.90[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9324212	0.95[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv2831	chr2:95618109-95662330	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv979060	chr2:95642571-95663204	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3408508	chr2:95658525-95662923	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4854241	CYP4F32P	cis	Esophagus Mucosa	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95651200-95660600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:95651600-95660600	Weak transcription	Esophagus	oesophagus

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