Variant report

Variant	rs12461802
Chromosome Location	chr19:21725407-21725408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11085456	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666680	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12609768	0.86[EUR][1000 genomes]
rs12610154	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12973084	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12974329	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12985995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401926	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879237	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879238	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2133822	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28898308	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34040704	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34497957	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35782355	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4462731	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56346453	0.80[AMR][1000 genomes]
rs6511255	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6511259	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7250360	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7250838	0.82[EUR][1000 genomes]
rs7251540	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7251669	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252254	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7253559	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7256389	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7257186	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259317	0.86[EUR][1000 genomes]
rs73017722	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8101089	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8101900	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8106840	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109536	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110459	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8110814	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8111885	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789284	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
10	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
11	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
12	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
13	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
14	nsv543945	chr19:21717518-21767567	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs12461802	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs12461802	RP11-678G14.2	cis	Thyroid	GTEx
rs12461802	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12461802	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs12461802	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs12461802	RP11-678G14.3	cis	lung	GTEx
rs12461802	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs12461802	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs12461802	RP11-678G14.2	cis	Whole Blood	GTEx
rs12461802	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12461802	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12461802	RP11-678G14.2	cis	lung	GTEx
rs12461802	CTD-2561J22.5	cis	lung	GTEx
rs12461802	RP11-420K14.3	cis	Whole Blood	GTEx
rs12461802	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs12461802	CTD-2561J22.5	cis	Thyroid	GTEx
rs12461802	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs12461802	RP11-420K14.2	cis	Whole Blood	GTEx
rs12461802	RP11-678G14.3	cis	Whole Blood	GTEx
rs12461802	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs12461802	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs12461802	ZNF100	cis	Muscle Skeletal	GTEx
rs12461802	ZNF429	cis	Whole Blood	GTEx
rs12461802	ZNF429	cis	Muscle Skeletal	GTEx
rs12461802	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs12461802	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs12461802	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12461802	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
2	chr19:21701000-21733400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21715200-21728600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:21719600-21729400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:21720000-21727400	Weak transcription	Brain Substantia Nigra	brain
6	chr19:21720400-21740800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:21720800-21725600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:21720800-21729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:21721600-21728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:21722800-21727200	Weak transcription	Osteobl	bone
11	chr19:21722800-21727600	Weak transcription	Psoas Muscle	Psoas
12	chr19:21724200-21725600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
13	chr19:21724200-21726000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
14	chr19:21724200-21726200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:21724200-21726200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:21724200-21726200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr19:21724200-21726400	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr19:21724200-21726600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:21724200-21727000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr19:21724200-21727200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:21724200-21727600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:21724200-21727800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:21724400-21726200	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:21724400-21726400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
25	chr19:21724400-21726600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr19:21724400-21727000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr19:21724400-21728200	ZNF genes & repeats	Fetal Brain Female	brain
28	chr19:21724600-21725600	Weak transcription	Dnd41	blood
29	chr19:21724600-21726000	ZNF genes & repeats	Lung	lung
30	chr19:21724600-21726000	Weak transcription	HSMM	muscle
31	chr19:21724600-21726200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:21724600-21726200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr19:21724600-21726200	ZNF genes & repeats	Aorta	Aorta
34	chr19:21724600-21726200	Strong transcription	Brain Anterior Caudate	brain
35	chr19:21724600-21726200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
36	chr19:21724600-21726200	ZNF genes & repeats	Gastric	stomach
37	chr19:21724600-21726200	ZNF genes & repeats	Left Ventricle	heart
38	chr19:21724600-21726200	Strong transcription	Ovary	ovary
39	chr19:21724600-21726200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr19:21724600-21726400	Strong transcription	Brain Germinal Matrix	brain
41	chr19:21724600-21726600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:21724600-21726800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
43	chr19:21724600-21727000	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr19:21724600-21727400	ZNF genes & repeats	Fetal Stomach	stomach
45	chr19:21724600-21727600	ZNF genes & repeats	Spleen	Spleen
46	chr19:21724600-21727800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:21724600-21728000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:21724600-21729800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr19:21724800-21725800	Strong transcription	Rectal Smooth Muscle	rectum
50	chr19:21724800-21726000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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