Variant report

Variant	rs2059901
Chromosome Location	chr16:72458155-72458156
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	chr16:72453071..72454725-chr16:72457023..72458717,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10400973	1.00[AFR][1000 genomes]
rs10492820	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11075930	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11075931	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11075934	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11075938	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11075940	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11531326	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12051317	0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12051376	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12051436	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12445485	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12595984	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12596421	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12596520	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12596827	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12597916	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12598100	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12599861	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12600175	0.85[AMR][1000 genomes]
rs12600298	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12708932	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12921040	1.00[AFR][1000 genomes]
rs1366847	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1437196	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1529527	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16970845	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970852	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16970879	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16970888	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16970895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16970901	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16970906	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16970922	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16970969	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16970987	0.91[ASN][1000 genomes]
rs16970998	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2043022	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2107153	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2161659	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2163067	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2860232	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2878752	1.00[AFR][1000 genomes]
rs28823672	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2884552	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28876074	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2905695	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2905696	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2914768	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2914770	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2914772	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2914773	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2914776	0.84[ASN][1000 genomes]
rs2914778	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2914781	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2967238	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967239	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4278755	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4788468	0.82[AMR][1000 genomes]
rs4788474	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788627	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4788629	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4788631	0.89[AMR][1000 genomes]
rs4788633	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4788634	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4788635	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4788637	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58097957	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs60144415	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60962205	0.91[AMR][1000 genomes]
rs6499575	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6499576	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6499578	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6499579	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7192128	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7194567	1.00[AFR][1000 genomes]
rs7405242	0.80[ASN][1000 genomes]
rs8048815	0.81[ASN][1000 genomes]
rs873899	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9927280	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9934215	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9935202	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9935250	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9936708	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][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	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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72443600-72461600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:72447600-72459400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:72451400-72459600	Weak transcription	Primary B cells from cord blood	blood
4	chr16:72453800-72458200	Weak transcription	Brain Hippocampus Middle	brain
5	chr16:72455200-72462600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:72455400-72459000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:72456400-72458800	ZNF genes & repeats	Dnd41	blood
8	chr16:72456600-72458600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr16:72457000-72459400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr16:72457000-72461600	Weak transcription	HepG2	liver
11	chr16:72457200-72467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr16:72457400-72459400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:72457600-72458600	Strong transcription	Primary hematopoietic stem cells	blood
14	chr16:72457600-72459400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:72457600-72460400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr16:72457800-72458400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr16:72457800-72458600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:72457800-72458800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr16:72457800-72461200	Weak transcription	Fetal Intestine Small	intestine
20	chr16:72457800-72461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr16:72457800-72462800	Weak transcription	Primary T cells from cord blood	blood
22	chr16:72458000-72458600	Enhancers	Brain Germinal Matrix	brain
23	chr16:72458000-72458800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr16:72458000-72458800	Enhancers	Fetal Brain Male	brain
25	chr16:72458000-72459000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr16:72458000-72459400	Weak transcription	Thymus	Thymus
27	chr16:72458000-72459600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:72458000-72461400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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