Variant report

Variant	rs6669608
Chromosome Location	chr1:152475233-152475234
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	chr1:152475128..152477150-chr1:152479048..152480719,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1001834	0.82[JPT][hapmap]
rs1053590	0.87[JPT][hapmap]
rs11205014	0.87[JPT][hapmap]
rs11205018	0.86[JPT][hapmap]
rs11581947	0.87[JPT][hapmap]
rs12132469	0.92[JPT][hapmap]
rs1415432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1538084	0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1885531	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1970283	0.82[JPT][hapmap]
rs2146120	0.95[ASN][1000 genomes]
rs2181173	0.86[EUR][1000 genomes]
rs3753451	0.87[JPT][hapmap]
rs477621	0.87[JPT][hapmap]
rs4845441	0.84[JPT][hapmap]
rs4845442	0.83[JPT][hapmap]
rs4845779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845780	0.84[JPT][hapmap]
rs4845782	0.81[JPT][hapmap]
rs4845783	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488393	0.87[JPT][hapmap]
rs493133	0.82[JPT][hapmap]
rs499697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs548252	0.87[JPT][hapmap]
rs574749	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6658925	0.87[JPT][hapmap]
rs6671924	0.85[JPT][hapmap]
rs7535188	0.85[EUR][1000 genomes]
rs908922	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1014393	chr1:152451935-152491693	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2750810	chr1:152453669-152660927	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1012908	chr1:152464844-152517845	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1005553	chr1:152464844-152519197	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv547859	chr1:152466882-152482587	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013357	chr1:152469744-152519184	Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1798404	chr1:152472839-152587113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1827111	chr1:152472839-152690073	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1830764	chr1:152472839-152690073	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr1:152471400-152478800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:152473200-152480600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:152473600-152476200	Enhancers	Placenta	Placenta
4	chr1:152473600-152480200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152473800-152475800	Flanking Active TSS	A549	lung
6	chr1:152473800-152478400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:152473800-152480600	Enhancers	HMEC	breast
8	chr1:152474000-152475400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:152474800-152475800	Weak transcription	Fetal Intestine Large	intestine
10	chr1:152475000-152475400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:152475000-152475400	Flanking Active TSS	NHEK	skin
12	chr1:152475200-152477200	Weak transcription	Esophagus	oesophagus

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