Variant report

Variant	rs11147402
Chromosome Location	chr13:30503872-30503873
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	chr13:30498204..30500565-chr13:30503827..30506540,2	MCF-7	breast:
2	chr13:30502030..30504176-chr13:30507351..30509428,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10467438	1.00[ASN][1000 genomes]
rs11147403	0.83[ASN][1000 genomes]
rs11619001	1.00[ASN][1000 genomes]
rs11619980	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620184	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803269	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803271	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475607	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs485057	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs486677	1.00[ASN][1000 genomes]
rs531084	1.00[ASN][1000 genomes]
rs548941	1.00[ASN][1000 genomes]
rs562459	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs565264	0.83[ASN][1000 genomes]
rs567291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs571307	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs572055	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs573132	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs584801	0.83[ASN][1000 genomes]
rs585231	0.83[ASN][1000 genomes]
rs586146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs586167	0.83[ASN][1000 genomes]
rs588372	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs602388	1.00[ASN][1000 genomes]
rs602884	1.00[ASN][1000 genomes]
rs605464	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs605478	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs618877	1.00[ASN][1000 genomes]
rs619367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs632214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs632258	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs633496	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs646983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs647794	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs651873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs662224	0.83[ASN][1000 genomes]
rs669105	1.00[ASN][1000 genomes]
rs679603	0.81[ASN][1000 genomes]
rs716801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs73159307	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338743	1.00[ASN][1000 genomes]
rs7358963	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7996122	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs818606	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs818607	0.83[ASN][1000 genomes]
rs818608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs865324	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs866019	1.00[ASN][1000 genomes]
rs912785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9285067	1.00[ASN][1000 genomes]
rs9285068	1.00[ASN][1000 genomes]
rs9578150	1.00[ASN][1000 genomes]
rs9579497	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9579501	1.00[ASN][1000 genomes]
rs9579505	1.00[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	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11147402	MTIF3	cis	parietal	SCAN
rs11147402	RNF6	cis	parietal	SCAN
rs11147402	LOC113230	trans	cerebellum	SCAN
rs11147402	ALOX5AP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30498400-30508000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr13:30498800-30513200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:30499000-30510000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr13:30499200-30509000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:30503200-30504000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:30503200-30504200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr13:30503400-30504000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:30503600-30504000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:30503600-30504000	Enhancers	NHEK	skin

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