Variant report

Variant	rs6511258
Chromosome Location	chr19:21694615-21694616
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10420016	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854048	0.81[ASN][1000 genomes]
rs10854050	0.85[ASN][1000 genomes]
rs10854051	0.85[ASN][1000 genomes]
rs11085462	0.85[ASN][1000 genomes]
rs11085465	0.85[ASN][1000 genomes]
rs11668606	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11671579	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12974758	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879234	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173727	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2359155	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562398	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562408	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562417	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562456	0.90[AMR][1000 genomes]
rs2562466	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562468	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562471	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562487	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2562507	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562508	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2650784	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2650792	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650793	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650804	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650805	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650825	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681370	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2681377	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681388	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2681389	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681391	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2681392	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681395	0.86[ASN][1000 genomes]
rs2946790	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35008138	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55771551	0.85[ASN][1000 genomes]
rs58001930	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62110163	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6511250	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6511253	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511254	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511256	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252585	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7259708	0.86[ASN][1000 genomes]
rs9304986	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304987	0.95[AMR][1000 genomes];0.92[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6511258	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs6511258	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs6511258	ZNF708	cis	lung	GTEx
rs6511258	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6511258	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs6511258	ZNF708	cis	Muscle Skeletal	GTEx
rs6511258	ZNF708	cis	Whole Blood	GTEx
rs6511258	RP11-678G14.3	cis	lung	GTEx
rs6511258	CTD-2561J22.5	cis	Thyroid	GTEx

Chromatin state (count:77 , 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	chr19:21689400-21694800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:21689400-21695200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:21689400-21698400	Weak transcription	Placenta	Placenta
6	chr19:21689400-21701200	Weak transcription	HSMMtube	muscle
7	chr19:21689400-21701600	Weak transcription	Brain Substantia Nigra	brain
8	chr19:21689400-21701600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:21689400-21702000	Weak transcription	Left Ventricle	heart
10	chr19:21689400-21702000	Weak transcription	Right Ventricle	heart
11	chr19:21689600-21695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:21689600-21700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:21689600-21701400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr19:21689600-21701600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:21689600-21702000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:21689800-21694800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr19:21689800-21695000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:21689800-21695600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:21689800-21696600	Weak transcription	Brain Anterior Caudate	brain
20	chr19:21689800-21697800	Weak transcription	Psoas Muscle	Psoas
21	chr19:21690000-21696200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:21690000-21701400	Weak transcription	Pancreas	Pancrea
23	chr19:21690000-21701600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:21690000-21701600	Weak transcription	Osteobl	bone
25	chr19:21690200-21698600	Weak transcription	Fetal Kidney	kidney
26	chr19:21690200-21701600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:21690200-21701600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr19:21690600-21694800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:21690600-21699600	Weak transcription	Primary T cells from cord blood	blood
30	chr19:21690600-21701600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr19:21690600-21701600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:21690800-21695000	Weak transcription	Fetal Stomach	stomach
33	chr19:21690800-21696600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:21690800-21696800	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:21691000-21694800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:21691000-21698400	Weak transcription	Fetal Lung	lung
37	chr19:21691200-21694800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:21691200-21694800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr19:21691200-21696600	Weak transcription	Gastric	stomach
40	chr19:21691200-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:21691200-21702000	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:21691400-21695000	Weak transcription	Primary B cells from cord blood	blood
43	chr19:21691400-21697000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr19:21691400-21701200	Weak transcription	Fetal Heart	heart
45	chr19:21691400-21701600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:21691400-21702000	Weak transcription	Ovary	ovary
47	chr19:21691600-21694800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:21691600-21699400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:21691600-21701000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:21692000-21696600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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