Variant report

Variant	rs2562413
Chromosome Location	chr19:21602886-21602887
allele	C/G
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: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10414834	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10424079	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666213	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666447	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666525	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666540	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11667103	0.83[EUR][1000 genomes]
rs11667361	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11669033	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11669790	0.83[EUR][1000 genomes]
rs11670815	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11670868	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11672341	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11672583	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11879901	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13346641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621154	0.83[EUR][1000 genomes]
rs1626404	0.83[EUR][1000 genomes]
rs1762578	0.83[EUR][1000 genomes]
rs17680605	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1781867	0.83[EUR][1000 genomes]
rs1781872	0.83[EUR][1000 genomes]
rs1967182	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061916	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2154302	0.81[EUR][1000 genomes]
rs2358993	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359144	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359145	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562405	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562411	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562416	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650776	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650844	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650848	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853837	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3853838	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4321312	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4327181	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4359573	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4544364	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4638726	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55756795	0.84[EUR][1000 genomes]
rs55790393	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55875743	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55899865	0.83[EUR][1000 genomes]
rs57299552	0.83[EUR][1000 genomes]
rs58412280	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60173523	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61035285	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62107465	0.81[EUR][1000 genomes]
rs62107469	0.81[EUR][1000 genomes]
rs62107472	0.83[EUR][1000 genomes]
rs62107479	0.84[EUR][1000 genomes]
rs62107531	0.84[EUR][1000 genomes]
rs62107532	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62107534	0.83[EUR][1000 genomes]
rs62107536	0.82[EUR][1000 genomes]
rs62107539	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62107540	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62107541	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109225	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109226	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62109227	0.83[AMR][1000 genomes]
rs62109228	0.83[AMR][1000 genomes]
rs62109229	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62110367	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62110377	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62110416	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110420	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110424	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110426	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110427	0.88[ASN][1000 genomes]
rs62110428	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110429	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7246339	0.83[EUR][1000 genomes]
rs7251135	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7258099	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7258473	0.85[EUR][1000 genomes]
rs7258562	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73537884	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8112786	1.00[YRI][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2562413	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2562413	RP11-678G14.2	cis	Whole Blood	GTEx
rs2562413	CTD-2561J22.5	cis	Thyroid	GTEx

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

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	chr19:21599600-21603000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:21599600-21603000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:21599600-21603000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
15	chr19:21599600-21603800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
16	chr19:21599600-21605200	ZNF genes & repeats	Fetal Intestine Small	intestine
17	chr19:21599600-21611000	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr19:21599800-21606400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr19:21599800-21606400	ZNF genes & repeats	Brain Germinal Matrix	brain
20	chr19:21600000-21603000	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr19:21600000-21613000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:21600200-21603000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
23	chr19:21600200-21606800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:21600200-21608200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:21600400-21605400	ZNF genes & repeats	Left Ventricle	heart
26	chr19:21600800-21603000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:21600800-21606600	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr19:21600800-21607800	ZNF genes & repeats	Dnd41	blood
29	chr19:21601000-21603000	ZNF genes & repeats	Brain Angular Gyrus	brain
30	chr19:21601200-21603800	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr19:21601200-21603800	ZNF genes & repeats	Ovary	ovary
32	chr19:21601200-21607600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
33	chr19:21601400-21603000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:21601600-21604400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:21601600-21605400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:21601800-21603000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:21601800-21603000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:21602000-21603800	ZNF genes & repeats	Pancreas	Pancrea
39	chr19:21602000-21604000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:21602000-21605000	Weak transcription	Fetal Heart	heart
41	chr19:21602000-21608200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr19:21602200-21603000	ZNF genes & repeats	Fetal Lung	lung
43	chr19:21602200-21603000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
44	chr19:21602200-21603200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
45	chr19:21602400-21603600	Weak transcription	Thymus	Thymus
46	chr19:21602600-21603000	ZNF genes & repeats	Fetal Intestine Large	intestine
47	chr19:21602800-21603600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:21602800-21603600	Weak transcription	Right Ventricle	heart
49	chr19:21602800-21604600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:21602800-21605000	Weak transcription	HSMM	muscle

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