Variant report

Variant	rs9925108
Chromosome Location	chr16:48545909-48545910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48419410..48421944-chr16:48545496..48547470,2	MCF-7	breast:
2	chr16:48486381..48489610-chr16:48544436..48547308,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1001872	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1004704	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11076569	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11641936	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11643514	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11648225	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11865776	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1566466	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1566467	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1948713	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062554	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2062555	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088753	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2088754	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4028695	0.89[CEU][hapmap]
rs4785244	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4785520	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4785521	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55745119	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55782524	0.81[AFR][1000 genomes]
rs6500390	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7184700	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7189631	0.89[EUR][1000 genomes]
rs7194822	0.81[EUR][1000 genomes]
rs7198420	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7202422	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7202699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206781	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8046716	0.85[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs8052026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8054389	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8056201	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8056346	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8057027	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8063059	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9888862	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9889065	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9889067	0.80[ASN][1000 genomes]
rs9921402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9923092	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925138	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9926683	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9933892	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9937129	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9939368	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9939554	0.81[EUR][1000 genomes]
rs9940599	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9941289	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv1800739	chr16:48418505-48560315	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv428658	chr16:48438656-48587750	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1065358	chr16:48513824-48554254	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1064323	chr16:48531171-48573066	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1060196	chr16:48531171-48578101	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48543600-48547400	Enhancers	Placenta	Placenta
2	chr16:48544400-48546000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:48544400-48546400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:48544400-48546800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:48544600-48546000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr16:48544600-48546200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr16:48544800-48546800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:48545000-48546000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:48545200-48546000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:48545400-48546200	Flanking Active TSS	NHEK	skin
11	chr16:48545800-48546800	Enhancers	HMEC	breast

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