Variant report

Variant	rs2562412
Chromosome Location	chr19:21602728-21602729
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21596819..21599115-chr19:21600673..21603133,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10410362	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10412054	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11878543	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11879647	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11880701	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11880751	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11881331	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11881379	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11882304	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1762561	1.00[AMR][1000 genomes]
rs1762562	1.00[AMR][1000 genomes]
rs1762569	1.00[AMR][1000 genomes]
rs1781849	1.00[AMR][1000 genomes]
rs1781854	1.00[AMR][1000 genomes]
rs1781859	1.00[AMR][1000 genomes]
rs1846713	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1909772	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1963057	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2011379	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2088759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173726	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2359147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434998	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2454922	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2537693	1.00[AMR][1000 genomes]
rs2537695	1.00[AMR][1000 genomes]
rs2562434	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2562460	0.84[EUR][1000 genomes]
rs2650772	0.84[EUR][1000 genomes]
rs2650811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650838	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2650839	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2801860	1.00[AMR][1000 genomes]
rs28857324	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2914643	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2914644	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2928219	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2928220	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2968029	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2968031	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2968071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35464445	1.00[ASN][1000 genomes]
rs57626552	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57847044	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58638125	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59087535	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59268487	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61062763	1.00[ASN][1000 genomes]
rs61334868	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7249229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73539807	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73543709	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73545768	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73545790	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73547713	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73547779	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73549716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
16	nsv578954	chr19:21587261-21604510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21590200-21606400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
6	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
7	chr19:21593600-21606600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:21598600-21603600	Weak transcription	Fetal Kidney	kidney
9	chr19:21598600-21605800	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:21599400-21603000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr19:21599400-21603200	ZNF genes & repeats	Fetal Brain Female	brain
12	chr19:21599600-21602800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:21599600-21603000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:21599600-21603000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:21599600-21603000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
16	chr19:21599600-21603800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr19:21599600-21605200	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr19:21599600-21611000	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr19:21599800-21606400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr19:21599800-21606400	ZNF genes & repeats	Brain Germinal Matrix	brain
21	chr19:21600000-21603000	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr19:21600000-21613000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:21600200-21602800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr19:21600200-21602800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
25	chr19:21600200-21603000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
26	chr19:21600200-21606800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:21600200-21608200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:21600400-21602800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
29	chr19:21600400-21602800	ZNF genes & repeats	Lung	lung
30	chr19:21600400-21605400	ZNF genes & repeats	Left Ventricle	heart
31	chr19:21600800-21603000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:21600800-21606600	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr19:21600800-21607800	ZNF genes & repeats	Dnd41	blood
34	chr19:21601000-21603000	ZNF genes & repeats	Brain Angular Gyrus	brain
35	chr19:21601200-21602800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:21601200-21602800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr19:21601200-21602800	ZNF genes & repeats	Fetal Stomach	stomach
38	chr19:21601200-21603800	ZNF genes & repeats	Fetal Muscle Leg	muscle
39	chr19:21601200-21603800	ZNF genes & repeats	Ovary	ovary
40	chr19:21601200-21607600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr19:21601400-21602800	ZNF genes & repeats	Brain Hippocampus Middle	brain
42	chr19:21601400-21603000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:21601600-21604400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:21601600-21605400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:21601800-21602800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
46	chr19:21601800-21603000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:21601800-21603000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:21602000-21603800	ZNF genes & repeats	Pancreas	Pancrea
49	chr19:21602000-21604000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:21602000-21605000	Weak transcription	Fetal Heart	heart

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