Variant report

Variant	rs8041420
Chromosome Location	chr15:39845090-39845091
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	chr15:39826333..39829143-chr15:39844610..39847564,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1551946	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969234	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969236	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969237	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16969251	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969254	1.00[ASN][1000 genomes]
rs1876850	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28390974	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28433877	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605448	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41519250	1.00[ASN][1000 genomes]
rs57247690	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57383264	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58042874	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58319120	1.00[ASN][1000 genomes]
rs58677957	1.00[ASN][1000 genomes]
rs58789628	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58886304	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59648752	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59948124	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60652586	0.91[AMR][1000 genomes]
rs61201811	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492901	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492904	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162555	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163169	1.00[ASN][1000 genomes]
rs7166970	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167206	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168679	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168836	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175706	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7183198	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385171	0.91[AMR][1000 genomes]
rs73385174	1.00[AMR][1000 genomes]
rs73385184	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385188	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385190	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387008	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387040	1.00[EUR][1000 genomes]
rs73387042	1.00[EUR][1000 genomes]
rs73387053	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387057	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387060	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387062	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387065	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387069	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389089	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389092	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389094	0.90[AMR][1000 genomes]
rs73389096	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73391204	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73391206	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73391226	1.00[ASN][1000 genomes]
rs73391234	1.00[ASN][1000 genomes]
rs8024038	0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024502	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024606	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024670	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024886	1.00[ASN][1000 genomes]
rs8038776	1.00[ASN][1000 genomes]
rs8039379	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937955	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9673056	0.87[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39839000-39848200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:39844400-39846000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:39844400-39851200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:39844600-39845400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr15:39844600-39845400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr15:39844600-39846000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:39844600-39849600	Enhancers	Colon Smooth Muscle	Colon
8	chr15:39844800-39845400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:39844800-39845600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr15:39844800-39846400	Enhancers	GM12878-XiMat	blood
11	chr15:39844800-39848600	Enhancers	Ovary	ovary
12	chr15:39844800-39849000	Enhancers	Fetal Lung	lung

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