Variant report

Variant	rs11584427
Chromosome Location	chr1:152299788-152299789
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	chr1:152297812..152299892-chr1:152301033..152302777,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10749669	0.92[CEU][hapmap]
rs10749670	0.93[CEU][hapmap];0.92[CHB][hapmap]
rs10788824	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs10888470	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs10888471	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs10888473	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs10888483	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204947	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs11204948	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs11204949	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11204976	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11204978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204980	0.93[CEU][hapmap];0.92[CHB][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204981	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11576858	0.82[AMR][1000 genomes]
rs11583524	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs11584340	0.93[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11586114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586631	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11587676	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11588170	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11588174	0.92[CEU][hapmap]
rs12405241	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12405278	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406105	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12407156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407553	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407748	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12407807	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730241	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1390488	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs1390490	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs1496045	0.92[CEU][hapmap]
rs1858479	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1858480	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1858482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2050631	0.98[ASN][1000 genomes]
rs2065955	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2065956	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184950	0.82[ASN][1000 genomes]
rs2184951	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2184953	0.80[CEU][hapmap];0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs2338555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338556	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3091276	0.80[EUR][1000 genomes]
rs3120659	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3120661	0.82[ASN][1000 genomes]
rs3120662	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3126058	0.81[ASN][1000 genomes]
rs3126060	0.81[ASN][1000 genomes]
rs3126062	0.82[ASN][1000 genomes]
rs3126066	0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3126067	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126072	0.81[EUR][1000 genomes]
rs3126074	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3126079	0.80[ASN][1000 genomes]
rs3126085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3126088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3126089	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3126091	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs3126092	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3126094	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3126095	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3126097	0.82[ASN][1000 genomes]
rs3126098	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34188926	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41267154	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4369233	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845423	0.92[CEU][hapmap]
rs4845736	1.00[CEU][hapmap]
rs4845745	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs4845750	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs55650366	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55654502	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58832908	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587666	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6661167	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666382	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs6681433	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6681457	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6683653	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71625202	0.81[AFR][1000 genomes]
rs72697000	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72698906	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74129461	0.82[AMR][1000 genomes]
rs7522925	0.84[EUR][1000 genomes]
rs7550106	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs877776	0.92[CEU][hapmap]
rs9436062	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv998298	chr1:152288685-152319877	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11584427	FLG	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152286600-152322200	Weak transcription	Ovary	ovary
2	chr1:152297800-152300000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:152298000-152301600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:152298200-152301000	Weak transcription	HMEC	breast
5	chr1:152298200-152301200	Weak transcription	NHEK	skin
6	chr1:152298200-152301600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:152299200-152300200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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