Variant report

Variant	rs9479403
Chromosome Location	chr6:150337746-150337747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150258514..150260378-chr6:150337573..150339969,2	MCF-7	breast:
2	chr6:150154861..150155845-chr6:150337730..150338274,2	K562	blood:
3	chr6:150246157..150249113-chr6:150336737..150339289,2	K562	blood:
4	chr6:150283429..150285848-chr6:150336024..150337757,2	MCF-7	breast:
5	chr6:150250322..150251340-chr6:150337738..150338572,3	K562	blood:
6	chr6:150323301..150326870-chr6:150337464..150339739,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111981	Chromatin interaction
ENSG00000218358	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10155731	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11155697	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11752529	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11752629	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11754987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11757186	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12204988	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13198863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13209192	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs1543547	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1853664	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34006533	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3860823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4086064	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5006620	0.93[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5017312	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5017313	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5017314	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5017315	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5017316	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs562425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs563278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61730071	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72561813	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9478354	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9478362	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478380	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9479404	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9479405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9479429	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9479478	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9479481	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9479482	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9479513	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv970176	chr6:150319173-150343329	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv7375	chr6:150324114-150388625	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3344440	chr6:150324131-150388650	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3323918	chr6:150327978-150392099	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv886766	chr6:150335407-150364009	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv886767	chr6:150335407-150400488	Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9479403	LATS1	cis	cerebellum	SCAN
rs9479403	UST	cis	cerebellum	SCAN
rs9479403	RAB32	cis	cerebellum	SCAN
rs9479403	C6orf72	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150335200-150340400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:150336800-150339800	Weak transcription	HMEC	breast
3	chr6:150337000-150338200	Enhancers	K562	blood
4	chr6:150337600-150338000	Bivalent Enhancer	Brain Angular Gyrus	brain
5	chr6:150337600-150338200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
6	chr6:150337600-150338200	Bivalent Enhancer	Brain Hippocampus Middle	brain
7	chr6:150337600-150338200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
8	chr6:150337600-150338200	Bivalent Enhancer	Brain Substantia Nigra	brain
9	chr6:150337600-150338200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle

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