Variant report

Variant	rs1455858
Chromosome Location	chr7:136631703-136631704
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	chr1:55333501..55334221-chr7:136631662..136632182,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10225215	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs10242108	0.82[CHB][hapmap]
rs1111418	0.88[CHD][hapmap]
rs1158586	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12155015	0.96[CEU][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs1364407	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1364409	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1378645	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378646	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378647	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1424386	0.82[CHB][hapmap]
rs1455857	1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1824024	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2350780	0.82[CHB][hapmap];0.83[MEX][hapmap]
rs2350783	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34135940	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6467695	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467696	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6942627	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6943950	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6945230	0.82[CHB][hapmap]
rs6952264	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6960707	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6963819	0.82[CHB][hapmap]
rs7782965	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7792449	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs978437	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831147	chr7:136583444-136755741	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1455858	PLXNA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136607800-136638000	Weak transcription	NHLF	lung
2	chr7:136623400-136641600	Weak transcription	Right Ventricle	heart
3	chr7:136623600-136641600	Weak transcription	Left Ventricle	heart
4	chr7:136631200-136632000	Enhancers	Fetal Heart	heart
5	chr7:136631400-136631800	Enhancers	Colon Smooth Muscle	Colon
6	chr7:136631600-136632000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr7:136631600-136636400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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