Variant report

Variant	rs7246839
Chromosome Location	chr19:53706544-53706545
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	chr19:53705415..53707075-chr19:53718366..53721132,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10775558	0.82[EUR][1000 genomes]
rs10853858	0.82[EUR][1000 genomes]
rs10853859	0.82[EUR][1000 genomes]
rs11084224	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11084225	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11084226	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1136205	0.81[EUR][1000 genomes]
rs11666072	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669455	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11670443	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11671568	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11671603	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11672910	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11879930	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11879932	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12462419	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462452	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462453	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462484	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12610332	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12982950	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17206931	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17272903	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34189836	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34535235	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35001955	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35121915	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35231505	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35653121	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4358051	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4449055	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4801964	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801965	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801966	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4801968	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4801970	0.82[EUR][1000 genomes]
rs4803064	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803065	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62117767	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6509733	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7245395	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7245485	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245880	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260577	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7260623	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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
rs7246839	ZNF818P	cis	Artery Tibial	GTEx
rs7246839	ZNF818P	cis	lung	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

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	chr19:53701400-53706600	Weak transcription	Fetal Kidney	kidney
11	chr19:53701400-53706600	Weak transcription	Psoas Muscle	Psoas
12	chr19:53701400-53706800	Weak transcription	Fetal Brain Male	brain
13	chr19:53701400-53707000	Weak transcription	Brain Germinal Matrix	brain
14	chr19:53701400-53708200	Weak transcription	Fetal Brain Female	brain
15	chr19:53701400-53709600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
16	chr19:53701400-53710200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
17	chr19:53701400-53715200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr19:53701600-53709200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:53701600-53710200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:53701600-53715400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
21	chr19:53701600-53720200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
22	chr19:53701600-53724800	ZNF genes & repeats	Liver	Liver
23	chr19:53701600-53725000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr19:53701600-53725000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:53701800-53709000	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr19:53701800-53718400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:53701800-53725400	ZNF genes & repeats	Adipose Nuclei	Adipose
28	chr19:53702000-53706600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:53702200-53709000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:53702200-53709000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
31	chr19:53702200-53709200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:53702200-53710200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:53702200-53715200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
34	chr19:53702400-53709600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
35	chr19:53702400-53724800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:53702600-53709200	ZNF genes & repeats	Placenta	Placenta
37	chr19:53703000-53707000	Strong transcription	Right Ventricle	heart
38	chr19:53703200-53709200	ZNF genes & repeats	Fetal Intestine Large	intestine
39	chr19:53703200-53709600	ZNF genes & repeats	Lung	lung
40	chr19:53703400-53709600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:53703400-53709600	ZNF genes & repeats	Esophagus	oesophagus
42	chr19:53703400-53709600	ZNF genes & repeats	Fetal Stomach	stomach
43	chr19:53703400-53715200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr19:53703600-53706600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr19:53703600-53709600	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr19:53703600-53715000	ZNF genes & repeats	Ovary	ovary
47	chr19:53704600-53706600	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:53704600-53707200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:53704600-53708000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:53704800-53706600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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