Variant report

Variant	rs28609100
Chromosome Location	chr1:153102158-153102159
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	chr1:153100002..153102988-chr20:52599879..52602542,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10157591	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1119652	0.86[AMR][1000 genomes]
rs11205205	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11205206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11205207	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11205212	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11205213	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12029300	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12035172	0.88[AMR][1000 genomes]
rs12036590	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12037255	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12040837	0.84[AMR][1000 genomes]
rs12045045	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12406869	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12408875	0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12409742	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12567386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12735128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13376230	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13376281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1500940	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16834968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16834971	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1926235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2291979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28664069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3766532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55676349	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57115197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58093379	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58339221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58665653	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58809172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60509474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60797518	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61204539	0.88[AMR][1000 genomes]
rs61315454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6679633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6692216	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72480208	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs735154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs74133286	0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7520621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7532449	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7534523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7541753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7541865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs904949	0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1004168	chr1:153088209-153226033	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153097400-153102800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:153097400-153104600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:153097400-153104600	Weak transcription	Pancreas	Pancrea
4	chr1:153099000-153104400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:153099000-153104400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:153099600-153104600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:153100000-153102200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:153100200-153102400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:153100200-153102800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:153100200-153102800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:153100200-153103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:153100200-153103200	Weak transcription	NHEK	skin
13	chr1:153100400-153102200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:153100400-153103200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:153100400-153103200	Weak transcription	HMEC	breast
16	chr1:153100400-153107000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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