Variant report

Variant	rs2681392
Chromosome Location	chr19:21695987-21695988
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10420016	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854048	0.81[ASN][1000 genomes]
rs10854050	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10854051	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085462	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085465	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11085468	0.81[EUR][1000 genomes]
rs11668606	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11671579	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12974758	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879234	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173727	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2359155	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562398	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562487	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2562507	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562508	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2650784	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650793	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650804	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650805	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681370	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681388	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2681389	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681391	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2681395	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2914646	0.92[AFR][1000 genomes]
rs2946790	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35008138	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35099594	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55771551	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58001930	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[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];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6511250	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511253	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511254	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511256	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511258	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252585	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259708	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304986	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304987	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2681392	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2681392	CTD-2561J22.5	cis	Thyroid	GTEx
rs2681392	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2681392	ZNF708	cis	Muscle Skeletal	GTEx
rs2681392	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2681392	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2681392	ZNF708	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21689200-21702000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21689200-21702000	Weak transcription	Stomach Mucosa	stomach
3	chr19:21689400-21698400	Weak transcription	Placenta	Placenta
4	chr19:21689400-21701200	Weak transcription	HSMMtube	muscle
5	chr19:21689400-21701600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:21689400-21701600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:21689400-21702000	Weak transcription	Left Ventricle	heart
8	chr19:21689400-21702000	Weak transcription	Right Ventricle	heart
9	chr19:21689600-21700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:21689600-21701400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr19:21689600-21701600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:21689600-21702000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:21689800-21696600	Weak transcription	Brain Anterior Caudate	brain
14	chr19:21689800-21697800	Weak transcription	Psoas Muscle	Psoas
15	chr19:21690000-21696200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr19:21690000-21701400	Weak transcription	Pancreas	Pancrea
17	chr19:21690000-21701600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:21690000-21701600	Weak transcription	Osteobl	bone
19	chr19:21690200-21698600	Weak transcription	Fetal Kidney	kidney
20	chr19:21690200-21701600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:21690200-21701600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:21690600-21699600	Weak transcription	Primary T cells from cord blood	blood
23	chr19:21690600-21701600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:21690600-21701600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr19:21690800-21696600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:21690800-21696800	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:21691000-21698400	Weak transcription	Fetal Lung	lung
28	chr19:21691200-21696600	Weak transcription	Gastric	stomach
29	chr19:21691200-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:21691200-21702000	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:21691400-21697000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr19:21691400-21701200	Weak transcription	Fetal Heart	heart
33	chr19:21691400-21701600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:21691400-21702000	Weak transcription	Ovary	ovary
35	chr19:21691600-21699400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:21691600-21701000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:21692000-21696600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:21692400-21701600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:21692600-21696200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:21693000-21698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:21693400-21696200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:21693400-21696200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:21693400-21696600	Weak transcription	Dnd41	blood
44	chr19:21694400-21697200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:21694600-21696000	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr19:21694600-21701000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:21694800-21696200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr19:21694800-21697000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:21695000-21696600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:21695000-21696600	Weak transcription	Duodenum Mucosa	Duodenum

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