Variant report

Variant	rs4780227
Chromosome Location	chr15:34507394-34507395
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	chr15:34402294..34404744-chr15:34506028..34509076,3	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10775222	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs10851952	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10851955	0.95[ASN][1000 genomes]
rs10851964	0.81[JPT][hapmap]
rs11073010	0.95[ASN][1000 genomes]
rs11073014	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11073019	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133154	0.85[CHD][hapmap]
rs11635964	0.86[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11636442	0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap]
rs11852537	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs11854686	0.86[ASN][1000 genomes]
rs11857205	0.86[ASN][1000 genomes]
rs11857684	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs11858408	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050753	0.85[CHD][hapmap]
rs12437551	0.92[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12441003	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12442758	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591181	0.84[JPT][hapmap]
rs12592460	0.81[ASN][1000 genomes]
rs12594077	0.92[CHB][hapmap]
rs12917397	0.94[ASN][1000 genomes]
rs16958835	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs16958836	0.84[CHB][hapmap]
rs16958878	0.85[CHD][hapmap]
rs17236777	0.85[CHD][hapmap]
rs17236784	0.85[CHD][hapmap]
rs17817806	0.88[CHD][hapmap]
rs1978810	0.92[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2244040	0.88[CHD][hapmap]
rs2290940	0.88[CHD][hapmap]
rs2290941	0.88[CHD][hapmap]
rs2290942	0.88[CHD][hapmap]
rs28652966	0.91[ASN][1000 genomes]
rs4238572	0.85[CHD][hapmap]
rs4381574	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4530104	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4577050	0.80[JPT][hapmap]
rs4780229	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4780231	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs56731918	0.90[ASN][1000 genomes]
rs57502425	0.84[ASN][1000 genomes]
rs58875083	0.90[ASN][1000 genomes]
rs6495619	0.83[ASN][1000 genomes]
rs6495620	0.81[ASN][1000 genomes]
rs6495621	0.84[ASN][1000 genomes]
rs6495622	0.87[GIH][hapmap]
rs6495625	0.86[ASN][1000 genomes]
rs7164448	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7168619	0.84[ASN][1000 genomes]
rs7168761	0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs7174014	0.83[ASN][1000 genomes]
rs7174442	0.92[CHB][hapmap];0.86[CHD][hapmap]
rs7178002	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs7178203	0.92[CHB][hapmap];0.86[CHD][hapmap]
rs7178988	0.92[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs7180200	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7180920	0.81[ASN][1000 genomes]
rs7181687	0.92[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs7181902	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs8025406	0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap]
rs8025730	0.92[CHB][hapmap]
rs8026939	0.91[ASN][1000 genomes]
rs8027499	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8027830	0.90[ASN][1000 genomes]
rs8034315	0.90[ASN][1000 genomes]
rs8035493	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs8035954	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs8036468	0.95[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040071	0.94[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs8040732	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs8041586	0.81[ASN][1000 genomes]
rs8041977	0.87[ASN][1000 genomes]
rs8043216	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9972505	0.92[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4780227	TRPM1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34502600-34510000	Weak transcription	NHLF	lung
2	chr15:34505000-34510200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:34506800-34507600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:34507000-34507400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr15:34507000-34508200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr15:34507000-34509600	Weak transcription	K562	blood
7	chr15:34507200-34507400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr15:34507200-34507600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr15:34507200-34508200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:34507200-34508200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr15:34507200-34516200	Weak transcription	H1 Cell Line	embryonic stem cell

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