Variant report

Variant	rs12462419
Chromosome Location	chr19:53708185-53708186
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	chr19:53700585..53702772-chr19:53706802..53709941,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10775558	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10853858	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10853859	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11084224	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11084225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084226	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1136205	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11666072	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11669455	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11670443	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671568	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11671603	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11672910	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11879930	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11879932	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462452	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462453	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462484	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610332	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982950	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17206931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17272903	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34189836	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34535235	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35001955	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35121915	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35231505	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35653121	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4358051	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449055	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4801964	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801965	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801966	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4801968	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4801969	0.86[ASN][1000 genomes]
rs4801970	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803064	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803065	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59782712	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62117767	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62117782	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6509733	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7245395	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7245485	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7245880	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7246839	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7260577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7260623	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2762999	chr19:53665818-53709353	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1065473	chr19:53680455-53709341	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv1060349	chr19:53682042-53709341	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12462419	ZNF818P	cis	lung	GTEx
rs12462419	ZNF818P	cis	Artery Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53700800-53708200	Weak transcription	Fetal Heart	heart
2	chr19:53700800-53709200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:53701000-53708800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:53701000-53709000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:53701000-53709200	ZNF genes & repeats	Fetal Intestine Small	intestine
6	chr19:53701000-53709600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:53701000-53710000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr19:53701200-53709600	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr19:53701200-53713200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:53701400-53708200	Weak transcription	Fetal Brain Female	brain
11	chr19:53701400-53709600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr19:53701400-53710200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
13	chr19:53701400-53715200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr19:53701600-53709200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:53701600-53710200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:53701600-53715400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
17	chr19:53701600-53720200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr19:53701600-53724800	ZNF genes & repeats	Liver	Liver
19	chr19:53701600-53725000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr19:53701600-53725000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr19:53701800-53709000	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr19:53701800-53718400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:53701800-53725400	ZNF genes & repeats	Adipose Nuclei	Adipose
24	chr19:53702200-53709000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:53702200-53709000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
26	chr19:53702200-53709200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:53702200-53710200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr19:53702200-53715200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
29	chr19:53702400-53709600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
30	chr19:53702400-53724800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:53702600-53709200	ZNF genes & repeats	Placenta	Placenta
32	chr19:53703200-53709200	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr19:53703200-53709600	ZNF genes & repeats	Lung	lung
34	chr19:53703400-53709600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:53703400-53709600	ZNF genes & repeats	Esophagus	oesophagus
36	chr19:53703400-53709600	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:53703400-53715200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr19:53703600-53709600	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr19:53703600-53715000	ZNF genes & repeats	Ovary	ovary
40	chr19:53705200-53715000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
41	chr19:53706000-53708600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:53706000-53709000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:53706000-53709800	ZNF genes & repeats	Fetal Lung	lung
44	chr19:53706200-53708800	ZNF genes & repeats	NHDF-Ad	bronchial
45	chr19:53706200-53709200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:53706200-53709200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr19:53706200-53709600	ZNF genes & repeats	Aorta	Aorta
48	chr19:53706200-53710000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr19:53706400-53709000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:53706400-53709200	ZNF genes & repeats	Colonic Mucosa	Colon

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