Variant report

Variant	rs540972
Chromosome Location	chr16:12418296-12418297
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12412998..12415794-chr16:12417822..12420522,2	MCF-7	breast:
2	chr16:12388084..12390009-chr16:12417985..12420361,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11075062	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11641317	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11641878	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11648926	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476117	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs158467	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16959342	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2013951	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209834	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209835	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209836	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209839	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209845	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209854	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2856766	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2856770	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476267	0.82[EUR][1000 genomes]
rs4781205	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4781211	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4781214	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs512286	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs544598	0.83[EUR][1000 genomes]
rs544673	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6498277	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7184369	0.88[EUR][1000 genomes]
rs7200289	0.82[ASN][1000 genomes]
rs7201621	0.84[AMR][1000 genomes]
rs7202201	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7203117	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8051010	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9635495	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv905349	chr16:12408750-12445863	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv827555	chr16:12413244-12429978	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
2	chr16:12404200-12427400	Weak transcription	Primary T cells from cord blood	blood
3	chr16:12405600-12426400	Weak transcription	Lung	lung
4	chr16:12405600-12442400	Weak transcription	Spleen	Spleen
5	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr16:12410200-12424400	Weak transcription	Right Atrium	heart
7	chr16:12410200-12464800	Weak transcription	Gastric	stomach
8	chr16:12414400-12431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:12414800-12432000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr16:12415000-12424600	Weak transcription	Esophagus	oesophagus
11	chr16:12415000-12431600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:12415400-12435400	Weak transcription	Pancreas	Pancrea
13	chr16:12415600-12421400	Weak transcription	Right Ventricle	heart
14	chr16:12415600-12425200	Weak transcription	Primary B cells from cord blood	blood
15	chr16:12415800-12421800	Weak transcription	Fetal Heart	heart
16	chr16:12416000-12423800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr16:12416200-12427600	Weak transcription	Thymus	Thymus
18	chr16:12416800-12438600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr16:12417000-12418400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:12417000-12418800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:12417400-12418400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr16:12417400-12418400	Enhancers	Brain Anterior Caudate	brain
23	chr16:12417400-12418400	Enhancers	Brain Substantia Nigra	brain
24	chr16:12417400-12418800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr16:12417600-12421000	Weak transcription	Ovary	ovary
26	chr16:12417600-12422400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr16:12417600-12422600	Weak transcription	GM12878-XiMat	blood
28	chr16:12417800-12418400	Enhancers	Adipose Nuclei	Adipose
29	chr16:12417800-12418400	Enhancers	Fetal Muscle Trunk	muscle
30	chr16:12417800-12418600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr16:12417800-12418600	Enhancers	Psoas Muscle	Psoas
32	chr16:12417800-12418800	Enhancers	Fetal Muscle Leg	muscle
33	chr16:12417800-12418800	Enhancers	Stomach Smooth Muscle	stomach
34	chr16:12417800-12424200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr16:12418000-12418400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr16:12418000-12418400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr16:12418000-12418400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr16:12418000-12418600	Enhancers	Left Ventricle	heart
39	chr16:12418200-12418400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr16:12418200-12418800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr16:12418200-12418800	Enhancers	Brain Hippocampus Middle	brain
42	chr16:12418200-12418800	Enhancers	HepG2	liver
43	chr16:12418200-12419000	Enhancers	Fetal Stomach	stomach
44	chr16:12418200-12419200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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