Variant report

Variant	rs28677977
Chromosome Location	chr16:72493371-72493372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1001493	0.83[AFR][1000 genomes]
rs1006805	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1013982	0.81[ASN][1000 genomes]
rs10852514	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11075935	0.88[EUR][1000 genomes]
rs11641842	0.83[AFR][1000 genomes]
rs11646282	0.88[EUR][1000 genomes]
rs11860023	0.85[AFR][1000 genomes]
rs11862324	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11865896	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12051542	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12149680	0.85[EUR][1000 genomes]
rs12445296	0.82[AFR][1000 genomes]
rs12596611	0.82[AFR][1000 genomes]
rs12598536	0.80[AFR][1000 genomes]
rs12598598	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12599375	0.95[AFR][1000 genomes]
rs13335806	0.86[AFR][1000 genomes]
rs1429072	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16970900	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16970908	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17841357	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1864229	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1864231	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1991530	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2079161	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2158265	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2158266	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2158268	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2860346	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2905697	0.93[AFR][1000 genomes]
rs2914769	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2914771	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2914774	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2914777	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2914779	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2967233	0.85[AFR][1000 genomes]
rs2967234	0.93[AFR][1000 genomes]
rs2967240	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4410082	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56152199	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56205630	0.81[AMR][1000 genomes]
rs56404261	0.86[AFR][1000 genomes]
rs62051139	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62052880	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7189331	0.84[AFR][1000 genomes]
rs7194470	0.86[AFR][1000 genomes]
rs7194533	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7204631	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8046070	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8046749	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8047866	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8049577	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8057278	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8060607	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8064129	0.82[AMR][1000 genomes]
rs806735	0.81[AMR][1000 genomes]
rs806739	0.81[AMR][1000 genomes]
rs806742	0.81[AMR][1000 genomes]
rs877641	0.90[AFR][1000 genomes]
rs9302637	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9922217	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9924296	0.88[AFR][1000 genomes]
rs9930813	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9936195	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1063172	chr16:72342110-72537808	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv542947	chr16:72342110-72537808	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1057127	chr16:72375524-72509686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv542949	chr16:72375524-72509686	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1055807	chr16:72418417-72614308	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv572956	chr16:72426448-72517014	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv523524	chr16:72464460-72635674	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1055142	chr16:72473520-72627783	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv542950	chr16:72473520-72627783	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72489200-72493400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:72489200-72495600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr16:72489600-72508400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr16:72490200-72493400	Weak transcription	Pancreas	Pancrea
5	chr16:72492800-72498600	Weak transcription	Primary B cells from cord blood	blood

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