Variant report

Variant	rs4419576
Chromosome Location	chr5:147532234-147532235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:147525612..147528709-chr5:147529097..147534248,4	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10061827	0.90[AFR][1000 genomes]
rs10065999	0.87[CEU][hapmap]
rs10067334	0.81[CEU][hapmap]
rs10068913	0.85[AFR][1000 genomes]
rs10068916	0.92[ASW][hapmap];0.86[CHD][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs10068988	0.85[ASW][hapmap];0.85[CEU][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs10070470	0.90[AFR][1000 genomes]
rs10075227	0.90[AFR][1000 genomes]
rs11168034	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13165271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13169394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13360182	0.80[CEU][hapmap]
rs1974627	0.82[AFR][1000 genomes]
rs2191680	0.85[CEU][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes]
rs2400488	0.90[AFR][1000 genomes]
rs2400491	0.90[AFR][1000 genomes]
rs2400492	0.90[AFR][1000 genomes]
rs2400493	0.82[AFR][1000 genomes]
rs2400496	0.82[AFR][1000 genomes]
rs3935572	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4254894	0.88[CEU][hapmap]
rs4269285	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[CHD][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs4270684	0.82[AFR][1000 genomes]
rs6881658	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs6888999	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6895745	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[CHD][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs724726	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767569	0.82[AFR][1000 genomes]
rs767570	0.82[AFR][1000 genomes]
rs7717500	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9285669	0.83[AFR][1000 genomes]
rs9325077	0.90[AFR][1000 genomes]
rs9325078	0.90[AFR][1000 genomes]
rs9885451	0.81[CEU][hapmap]

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	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4419576	SPINK6	cis	Esophagus Mucosa	GTEx
rs4419576	TFF3	trans	cerebellum	SCAN
rs4419576	SPINK1	cis	cerebellum	SCAN
rs4419576	FFAR2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147527800-147532400	Weak transcription	Fetal Intestine Large	intestine
2	chr5:147528000-147533200	Weak transcription	Fetal Intestine Small	intestine

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