Variant report

Variant	rs2562471
Chromosome Location	chr19:21715819-21715820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10420016	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10854048	0.80[ASN][1000 genomes]
rs10854050	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10854051	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085462	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085465	0.85[ASN][1000 genomes]
rs11668606	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11671579	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12974758	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879234	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173727	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2359155	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562398	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562417	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562456	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562487	0.81[AMR][1000 genomes]
rs2562507	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562508	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2650784	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650792	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2650793	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650804	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650805	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2650825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681370	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681388	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2681389	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681391	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2681392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681395	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2914646	0.92[AFR][1000 genomes]
rs2946790	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35008138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35099594	0.81[AMR][1000 genomes]
rs55771551	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58001930	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62109226	0.83[AFR][1000 genomes]
rs62109227	0.83[AFR][1000 genomes]
rs62109228	0.83[AFR][1000 genomes]
rs62110163	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511250	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6511253	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511254	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511256	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6511258	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7252585	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7259708	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9304986	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304987	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
6	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
7	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
8	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS 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
14	nsv543943	chr19:21713945-21759080	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv543944	chr19:21713945-21767567	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2562471	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2562471	ZNF708	cis	lung	GTEx
rs2562471	ZNF708	cis	Muscle Skeletal	GTEx
rs2562471	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2562471	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2562471	CTD-2561J22.5	cis	Thyroid	GTEx
rs2562471	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21699600-21720800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
3	chr19:21701000-21733400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:21701600-21720400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:21702400-21721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:21702600-21717200	Weak transcription	Psoas Muscle	Psoas
7	chr19:21702800-21717200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:21702800-21718600	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:21702800-21718600	Weak transcription	Fetal Heart	heart
10	chr19:21704000-21717200	Weak transcription	NHDF-Ad	bronchial
11	chr19:21705000-21718600	Weak transcription	HSMM	muscle
12	chr19:21706400-21717200	Weak transcription	K562	blood
13	chr19:21707000-21719000	Weak transcription	Stomach Mucosa	stomach
14	chr19:21708200-21716200	Strong transcription	Dnd41	blood
15	chr19:21708200-21717400	Strong transcription	Placenta	Placenta
16	chr19:21709000-21722800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:21709600-21716800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr19:21709600-21717200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:21710600-21717200	Weak transcription	NH-A	brain
20	chr19:21711600-21716400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:21711600-21720400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:21711800-21717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:21712000-21719200	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:21712200-21716800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:21712400-21720400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
26	chr19:21712600-21716200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
27	chr19:21712600-21716600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr19:21712600-21720200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
29	chr19:21713200-21717200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:21713400-21716600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:21713400-21717200	Strong transcription	Brain Angular Gyrus	brain
32	chr19:21713400-21717400	Strong transcription	Brain Germinal Matrix	brain
33	chr19:21713400-21719600	Strong transcription	Ovary	ovary
34	chr19:21713400-21720200	ZNF genes & repeats	Fetal Intestine Large	intestine
35	chr19:21713400-21720400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:21713400-21720800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:21713400-21720800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:21713400-21721800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:21713400-21722000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
40	chr19:21713400-21722800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:21713600-21716600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr19:21713800-21717000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr19:21714200-21716400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:21714200-21716400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:21714200-21717200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:21714200-21717200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr19:21714200-21717200	Weak transcription	Gastric	stomach
48	chr19:21714200-21717200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:21714200-21717200	Weak transcription	Spleen	Spleen
50	chr19:21714200-21717200	Weak transcription	HSMMtube	muscle

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