Variant report

Variant	rs1449090
Chromosome Location	chr2:187635712-187635713
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	chr2:187627243..187630051-chr2:187634032..187636877,3	MCF-7	breast:
2	chr2:187557380..187558959-chr2:187635555..187637431,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144369	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1349170	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1449088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1449091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1470602	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16828108	1.00[CHB][hapmap]
rs1839122	1.00[CHB][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2122177	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2247924	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442316	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442318	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2594702	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2594703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2594704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2595377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2595379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2595388	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682852	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2682853	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2682854	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682858	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2682859	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682860	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2682866	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682869	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2682870	1.00[CHB][hapmap]
rs2682872	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3738918	1.00[CHB][hapmap]
rs3754584	1.00[CHB][hapmap]
rs4309547	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57306419	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59855103	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73035695	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556971	1.00[CHB][hapmap]
rs976693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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	nsv428069	chr2:187575692-187766209	ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3495864	chr2:187633495-187686087	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3495865	chr2:187633495-187686087	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187612000-187636200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:187622600-187636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:187623000-187636200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:187627200-187636800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:187634400-187636000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:187635000-187636200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:187635000-187636800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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