Variant report

Variant	rs62110246
Chromosome Location	chr19:21787169-21787170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11085483	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11665855	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880659	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11881567	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883394	0.82[ASN][1000 genomes]
rs12459722	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462147	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2176802	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809145	0.82[ASN][1000 genomes]
rs57879343	0.83[ASN][1000 genomes]
rs58463686	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58952031	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60200684	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60206762	0.83[ASN][1000 genomes]
rs60223275	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61056366	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108369	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62108374	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62110214	0.82[ASN][1000 genomes]
rs950504	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1056332	chr19:21746555-21807647	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv911423	chr19:21783995-21858994	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62110246	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs62110246	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs62110246	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs62110246	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs62110246	RP11-678G14.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21784600-21787200	Enhancers	Fetal Intestine Large	intestine
2	chr19:21784800-21788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:21785400-21788200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:21786000-21788000	Flanking Active TSS	K562	blood
5	chr19:21786000-21788200	Flanking Active TSS	Dnd41	blood
6	chr19:21786200-21787200	Enhancers	Fetal Heart	heart
7	chr19:21786200-21787200	Enhancers	Gastric	stomach
8	chr19:21786200-21787800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:21786200-21787800	Enhancers	Spleen	Spleen
10	chr19:21786200-21788000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:21786200-21788200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr19:21786200-21788400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:21786400-21787200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:21786400-21787400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr19:21786400-21788200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr19:21786600-21787200	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr19:21786600-21787200	Enhancers	Fetal Brain Female	brain
18	chr19:21786600-21787200	Enhancers	Lung	lung
19	chr19:21786600-21787200	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr19:21786600-21787400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:21786600-21787400	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr19:21786600-21787400	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr19:21786600-21787400	Flanking Active TSS	Fetal Kidney	kidney
24	chr19:21786600-21787600	Active TSS	NHEK	skin
25	chr19:21786600-21787800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:21786600-21788200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:21786600-21788200	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr19:21786600-21788200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr19:21786800-21787200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr19:21786800-21787200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr19:21786800-21787200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:21786800-21787200	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr19:21786800-21787200	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr19:21786800-21787200	Flanking Active TSS	Thymus	Thymus
35	chr19:21786800-21787400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr19:21786800-21787400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr19:21786800-21787400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr19:21786800-21787400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr19:21786800-21787400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:21786800-21787600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:21786800-21787600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:21786800-21787600	Bivalent/Poised TSS	HepG2	liver
43	chr19:21786800-21787800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:21786800-21787800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:21786800-21787800	Active TSS	Muscle Satellite Cultured Cells	--
46	chr19:21786800-21787800	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr19:21786800-21787800	Active TSS	Osteobl	bone
48	chr19:21786800-21788000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr19:21786800-21788000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:21786800-21788000	Active TSS	Rectal Mucosa Donor 29	rectum

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