Variant report

Variant	rs12608652
Chromosome Location	chr19:21332807-21332808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10406253	0.94[JPT][hapmap]
rs10408496	0.93[JPT][hapmap]
rs10414473	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10415009	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10854042	0.93[JPT][hapmap]
rs11668640	0.81[AFR][1000 genomes]
rs11671623	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12980860	0.81[AFR][1000 genomes]
rs2115498	0.94[JPT][hapmap];0.86[YRI][hapmap]
rs4324267	0.82[JPT][hapmap]
rs6511202	0.94[JPT][hapmap]
rs6511204	0.94[JPT][hapmap];0.96[YRI][hapmap]
rs6511205	0.94[JPT][hapmap];0.97[YRI][hapmap];0.81[AFR][1000 genomes]
rs6511206	0.94[JPT][hapmap]
rs6511207	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7247730	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7250987	0.94[JPT][hapmap]
rs7251158	0.94[JPT][hapmap]
rs7251646	0.94[JPT][hapmap]
rs7254094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256576	0.94[JPT][hapmap]
rs7257196	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7258575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259368	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8101918	1.00[JPT][hapmap];0.97[YRI][hapmap];0.81[AFR][1000 genomes]
rs8108314	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking 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	25 gene(s)	inside rSNPs	diseases
3	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1065384	chr19:21249321-21350698	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv911413	chr19:21263518-21347598	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3319019	chr19:21268262-21336383	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3319020	chr19:21268262-21336383	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	esv5909	chr19:21272333-21334753	Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	esv3420290	chr19:21272477-21336432	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	esv3391713	chr19:21272485-21334631	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	esv5243	chr19:21272548-21334670	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	esv7204	chr19:21274198-21336396	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12608652	ZNF493	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21325400-21361800	Weak transcription	Small Intestine	intestine
2	chr19:21325600-21334200	Weak transcription	Psoas Muscle	Psoas
3	chr19:21325600-21365800	Weak transcription	Brain Angular Gyrus	brain
4	chr19:21326000-21337000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21326000-21338400	Weak transcription	Aorta	Aorta
6	chr19:21326000-21352600	Weak transcription	Right Ventricle	heart
7	chr19:21326000-21361000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:21326200-21333800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:21326200-21336200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr19:21326200-21336200	Strong transcription	Adipose Nuclei	Adipose
11	chr19:21326200-21336800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:21326200-21337000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:21326400-21333000	Strong transcription	Fetal Kidney	kidney
14	chr19:21326400-21334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:21326400-21335200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr19:21326400-21336200	Strong transcription	Fetal Lung	lung
17	chr19:21326400-21336600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:21326600-21336200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:21326600-21336400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr19:21326600-21337000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:21326800-21333200	ZNF genes & repeats	Dnd41	blood
22	chr19:21326800-21333800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:21326800-21336200	Strong transcription	HSMMtube	muscle
24	chr19:21326800-21336400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr19:21326800-21336400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:21326800-21361800	Weak transcription	Stomach Mucosa	stomach
27	chr19:21327000-21336400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:21327000-21336600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:21327000-21337000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:21327000-21342800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:21327000-21347000	Weak transcription	Hela-S3	cervix
32	chr19:21327400-21336200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:21327400-21336600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:21327400-21336800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:21327400-21336800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr19:21327600-21337000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:21327800-21336200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:21328000-21333000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:21328200-21333200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr19:21328200-21333200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:21328200-21334800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:21328200-21337000	ZNF genes & repeats	Fetal Brain Female	brain
43	chr19:21328400-21333000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr19:21328800-21336800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:21329200-21333400	Strong transcription	HUVEC	blood vessel
46	chr19:21329200-21335000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr19:21329200-21336200	Strong transcription	K562	blood
48	chr19:21329400-21336000	ZNF genes & repeats	Brain Germinal Matrix	brain
49	chr19:21329800-21334600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr19:21329800-21335800	Strong transcription	HSMM	muscle

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