Variant report

Variant	rs12973307
Chromosome Location	chr19:37103244-37103245
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10411411	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1053064	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12162275	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981751	0.88[AFR][1000 genomes]
rs2385640	0.83[ASN][1000 genomes]
rs2462576	0.82[ASN][1000 genomes]
rs2912401	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2912402	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2912406	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2912416	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912417	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967424	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967455	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967470	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096621	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096626	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108169	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108170	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108175	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108180	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108198	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108199	0.86[EUR][1000 genomes]
rs3108200	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108207	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108213	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108547	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108548	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108551	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108553	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108554	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108558	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108561	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108571	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108578	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108581	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108582	0.83[ASN][1000 genomes]
rs3108587	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108588	0.83[ASN][1000 genomes]
rs3108595	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108599	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108601	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3108611	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3111543	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3111545	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3111546	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71337534	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7254978	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112546	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826986	0.83[ASN][1000 genomes]
rs865448	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers 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	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic 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	73 gene(s)	inside rSNPs	diseases
7	esv3434386	chr19:37073454-37114509	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12973307	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37096800-37104000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:37096800-37110000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:37097000-37104400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:37097000-37106000	Weak transcription	Fetal Thymus	thymus
5	chr19:37097000-37106800	Weak transcription	Stomach Mucosa	stomach
6	chr19:37097000-37107000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:37097000-37107000	Weak transcription	Small Intestine	intestine
8	chr19:37097000-37107400	Weak transcription	HUVEC	blood vessel
9	chr19:37097000-37107800	Weak transcription	Gastric	stomach
10	chr19:37097000-37112600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:37097200-37104400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:37097200-37104800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:37097200-37105600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:37097200-37109600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr19:37097200-37110000	Weak transcription	NHLF	lung
16	chr19:37097400-37105200	Weak transcription	HepG2	liver
17	chr19:37098000-37103400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:37098000-37103600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:37098000-37104600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:37098000-37106200	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:37098000-37118200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:37098200-37103400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:37098200-37108400	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr19:37098200-37120400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:37098400-37103400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr19:37098400-37104000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:37098400-37105000	ZNF genes & repeats	Liver	Liver
29	chr19:37098400-37107400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:37098600-37104000	Strong transcription	Brain Anterior Caudate	brain
31	chr19:37098600-37104000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:37098600-37105200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:37098600-37105600	Strong transcription	Brain Angular Gyrus	brain
34	chr19:37098600-37106200	Strong transcription	Ovary	ovary
35	chr19:37098800-37103400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr19:37098800-37104000	Strong transcription	Brain Germinal Matrix	brain
37	chr19:37098800-37105000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:37098800-37106000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:37098800-37108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:37099000-37105600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:37099000-37109200	Strong transcription	Dnd41	blood
42	chr19:37099200-37105800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:37099200-37110000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr19:37099400-37103400	Strong transcription	Fetal Lung	lung
45	chr19:37099400-37103600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:37099600-37103600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:37099600-37103600	Strong transcription	Placenta	Placenta
48	chr19:37099600-37105800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:37099600-37108400	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:37100200-37107600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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