Variant report

Variant	rs1580288
Chromosome Location	chr3:110703523-110703524
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	chr3:110700773..110702681-chr3:110702725..110705258,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1075303	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919892	0.82[AFR][1000 genomes]
rs11927478	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060876	0.81[AFR][1000 genomes]
rs13061640	0.81[AFR][1000 genomes]
rs1350980	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1381828	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382075	0.81[AFR][1000 genomes]
rs1462789	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1462790	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1462793	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1462795	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1462801	0.85[EUR][1000 genomes]
rs1462807	0.91[ASN][1000 genomes]
rs1477841	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1477842	0.87[YRI][hapmap]
rs1477843	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1477847	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1477851	1.00[YRI][hapmap]
rs1477854	0.82[AFR][1000 genomes]
rs1477855	0.82[AFR][1000 genomes]
rs1585594	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1585595	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1599663	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1599664	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1600059	0.82[AFR][1000 genomes]
rs16857483	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824666	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903755	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1903759	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1993802	0.85[EUR][1000 genomes]
rs1993803	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2002969	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100875	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2126710	0.81[AFR][1000 genomes]
rs2126713	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs2399367	0.89[ASN][1000 genomes]
rs2399368	0.89[ASN][1000 genomes]
rs2399370	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2399371	0.82[EUR][1000 genomes]
rs2399373	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs2399378	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895376	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35665971	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4102676	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234401	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682028	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682215	0.89[ASN][1000 genomes]
rs4682229	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs4682230	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs4682231	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs4682234	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs4682238	1.00[YRI][hapmap]
rs5000277	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437940	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6437948	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs66513024	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67056469	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765948	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6781480	0.81[AFR][1000 genomes]
rs67832786	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6787921	0.90[ASN][1000 genomes]
rs6794645	1.00[YRI][hapmap]
rs6805399	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808847	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs723023	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs723025	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430600	1.00[YRI][hapmap]
rs7610760	0.94[YRI][hapmap]
rs7612667	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs7622983	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623003	0.85[EUR][1000 genomes]
rs7623064	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623103	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623880	1.00[YRI][hapmap]
rs7632375	0.81[AFR][1000 genomes]
rs7632388	0.81[AFR][1000 genomes]
rs7637068	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644948	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653595	0.95[CHB][hapmap];0.93[YRI][hapmap]
rs9817950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9821335	0.95[CHB][hapmap];0.93[YRI][hapmap]
rs9826064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828899	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs9837377	0.82[AFR][1000 genomes]
rs9839299	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9839674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847598	0.82[AFR][1000 genomes]
rs9866028	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs9876350	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs9876543	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877855	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv829674	chr3:110616256-110771049	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110703200-110703800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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