Variant report

Variant	rs209854
Chromosome Location	chr16:12407163-12407164
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	chr16:12405145..12407568-chr16:12414371..12416056,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11075062	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11641317	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11641878	0.85[EUR][1000 genomes]
rs11648926	0.83[AMR][1000 genomes]
rs1476117	0.82[EUR][1000 genomes]
rs158467	0.86[EUR][1000 genomes]
rs16959342	0.83[EUR][1000 genomes]
rs176717	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2013951	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209834	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209835	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209836	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209839	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209845	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209849	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs209850	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs209853	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs209855	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs209856	0.81[EUR][1000 genomes]
rs2856766	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2856770	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4781205	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4781211	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4781214	0.87[EUR][1000 genomes]
rs512286	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs540972	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs544673	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6498277	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7184369	0.82[EUR][1000 genomes]
rs7200289	0.90[ASN][1000 genomes]
rs7202201	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7203117	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7500910	0.81[ASN][1000 genomes]
rs8051010	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9635495	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12359800-12418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
3	chr16:12373400-12414200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr16:12374200-12417200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:12383200-12407800	Weak transcription	Gastric	stomach
6	chr16:12384400-12409000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr16:12385800-12410800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:12388600-12408200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:12395000-12409200	Weak transcription	Liver	Liver
10	chr16:12395400-12408000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr16:12395400-12413800	Weak transcription	Left Ventricle	heart
12	chr16:12395600-12408200	Weak transcription	Pancreas	Pancrea
13	chr16:12395600-12409400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:12395600-12417200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr16:12396000-12414800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr16:12396200-12414000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr16:12396800-12416400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr16:12397200-12407400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr16:12397800-12408200	Weak transcription	GM12878-XiMat	blood
20	chr16:12399400-12407200	Weak transcription	HepG2	liver
21	chr16:12399600-12407800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:12399800-12408000	Weak transcription	NHEK	skin
23	chr16:12399800-12408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr16:12401200-12409000	Weak transcription	Brain Germinal Matrix	brain
25	chr16:12403200-12408400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr16:12404000-12414800	Weak transcription	Thymus	Thymus
27	chr16:12404200-12407800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr16:12404200-12427400	Weak transcription	Primary T cells from cord blood	blood
29	chr16:12404400-12407800	Weak transcription	Primary B cells from cord blood	blood
30	chr16:12404600-12413400	Weak transcription	Fetal Heart	heart
31	chr16:12405200-12408400	Weak transcription	Colon Smooth Muscle	Colon
32	chr16:12405200-12411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr16:12405400-12407400	Weak transcription	Right Atrium	heart
34	chr16:12405600-12408600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr16:12405600-12409000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr16:12405600-12409400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr16:12405600-12409800	Weak transcription	Ovary	ovary
38	chr16:12405600-12410400	Weak transcription	Esophagus	oesophagus
39	chr16:12405600-12412800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr16:12405600-12413200	Weak transcription	Right Ventricle	heart
41	chr16:12405600-12426400	Weak transcription	Lung	lung
42	chr16:12405600-12442400	Weak transcription	Spleen	Spleen
43	chr16:12405800-12408200	Weak transcription	Stomach Mucosa	stomach
44	chr16:12405800-12408400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr16:12405800-12409000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr16:12405800-12413200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr16:12405800-12417800	Weak transcription	Adipose Nuclei	Adipose
48	chr16:12406200-12408200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr16:12406200-12408200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr16:12406200-12413200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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