Variant report

Variant	rs11804354
Chromosome Location	chr1:152874445-152874446
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	chr1:152872190..152876672-chr1:152877317..152882225,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163207	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10399761	1.00[EUR][1000 genomes]
rs10399933	1.00[EUR][1000 genomes]
rs10399958	1.00[EUR][1000 genomes]
rs11205123	1.00[EUR][1000 genomes]
rs11205124	1.00[EUR][1000 genomes]
rs11205125	1.00[EUR][1000 genomes]
rs11800110	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11802167	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802181	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802222	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11803737	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11804404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805389	1.00[EUR][1000 genomes]
rs11805896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807457	1.00[EUR][1000 genomes]
rs11807486	1.00[EUR][1000 genomes]
rs11807888	1.00[EUR][1000 genomes]
rs11809092	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11809110	0.84[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809520	1.00[EUR][1000 genomes]
rs11811489	1.00[EUR][1000 genomes]
rs11811567	1.00[EUR][1000 genomes]
rs12073467	1.00[CEU][hapmap]
rs12081164	1.00[EUR][1000 genomes]
rs12083273	1.00[EUR][1000 genomes]
rs12240158	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12403761	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16834574	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834582	1.00[CEU][hapmap]
rs16834595	1.00[CEU][hapmap]
rs16834596	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834611	1.00[CEU][hapmap]
rs16834716	1.00[EUR][1000 genomes]
rs16834719	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834732	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834736	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16834740	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16834743	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2879460	1.00[EUR][1000 genomes]
rs35920563	1.00[EUR][1000 genomes]
rs4378153	1.00[CEU][hapmap]
rs57938862	1.00[EUR][1000 genomes]
rs57942491	1.00[EUR][1000 genomes]
rs58015557	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58437291	1.00[EUR][1000 genomes]
rs58540020	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58862899	1.00[EUR][1000 genomes]
rs59008684	1.00[EUR][1000 genomes]
rs59343658	1.00[EUR][1000 genomes]
rs59441715	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59610990	1.00[EUR][1000 genomes]
rs59649412	1.00[EUR][1000 genomes]
rs60459088	1.00[EUR][1000 genomes]
rs60513675	1.00[EUR][1000 genomes]
rs61095410	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61146280	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61744935	1.00[EUR][1000 genomes]
rs61744941	1.00[EUR][1000 genomes]
rs6659570	1.00[EUR][1000 genomes]
rs6659675	1.00[EUR][1000 genomes]
rs6665277	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668146	1.00[EUR][1000 genomes]
rs6670654	1.00[EUR][1000 genomes]
rs6673420	1.00[CEU][hapmap]
rs6674372	1.00[CEU][hapmap]
rs6684782	1.00[CEU][hapmap]
rs6693942	1.00[EUR][1000 genomes]
rs6699386	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6703505	1.00[CEU][hapmap]
rs73006504	1.00[EUR][1000 genomes]
rs73006519	1.00[EUR][1000 genomes]
rs73006523	1.00[EUR][1000 genomes]
rs73006525	1.00[EUR][1000 genomes]
rs73006526	1.00[EUR][1000 genomes]
rs73006527	1.00[EUR][1000 genomes]
rs73006537	1.00[EUR][1000 genomes]
rs73006539	1.00[EUR][1000 genomes]
rs73006549	1.00[EUR][1000 genomes]
rs73006550	1.00[EUR][1000 genomes]
rs73006559	1.00[EUR][1000 genomes]
rs73006561	1.00[EUR][1000 genomes]
rs73006562	1.00[EUR][1000 genomes]
rs73006564	1.00[EUR][1000 genomes]
rs73006565	1.00[EUR][1000 genomes]
rs73006567	1.00[EUR][1000 genomes]
rs73006568	1.00[EUR][1000 genomes]
rs73006569	1.00[EUR][1000 genomes]
rs73006570	1.00[EUR][1000 genomes]
rs73006571	1.00[EUR][1000 genomes]
rs73006574	1.00[EUR][1000 genomes]
rs73006575	1.00[EUR][1000 genomes]
rs73008506	1.00[EUR][1000 genomes]
rs73021110	1.00[EUR][1000 genomes]
rs73021114	1.00[EUR][1000 genomes]
rs73021163	1.00[EUR][1000 genomes]
rs73021185	1.00[EUR][1000 genomes]
rs73023030	1.00[EUR][1000 genomes]
rs7530135	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv998873	chr1:152869127-152975258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152872600-152876600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:152873400-152874800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:152873800-152874800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:152873800-152874800	Enhancers	NHEK	skin
5	chr1:152874000-152874800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:152874000-152876000	Enhancers	Esophagus	oesophagus
7	chr1:152874200-152876400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:152874200-152876600	Weak transcription	GM12878-XiMat	blood

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