Variant report

Variant	rs3111549
Chromosome Location	chr19:37103778-37103779
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10402486	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10407386	0.83[EUR][1000 genomes]
rs11084862	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12610353	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1830031	0.85[EUR][1000 genomes]
rs2033077	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2217081	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2385642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385643	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096617	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3096618	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096619	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096622	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096623	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096627	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096628	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3096629	0.88[ASN][1000 genomes]
rs3096630	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096631	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096632	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096633	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3096635	0.84[EUR][1000 genomes]
rs3096636	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108166	0.94[EUR][1000 genomes]
rs3108167	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108168	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108171	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108172	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3108174	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108179	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108181	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108182	0.88[EUR][1000 genomes]
rs3108184	0.88[EUR][1000 genomes]
rs3108185	0.88[EUR][1000 genomes]
rs3108186	0.88[EUR][1000 genomes]
rs3108187	0.88[EUR][1000 genomes]
rs3108188	0.88[EUR][1000 genomes]
rs3108189	0.87[EUR][1000 genomes]
rs3108190	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108191	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108192	0.83[EUR][1000 genomes]
rs3108193	0.94[EUR][1000 genomes]
rs3108197	0.85[EUR][1000 genomes]
rs3108201	0.85[EUR][1000 genomes]
rs3108203	0.94[EUR][1000 genomes]
rs3108205	0.88[EUR][1000 genomes]
rs3108208	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3108209	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3108214	0.85[EUR][1000 genomes]
rs3108215	0.85[EUR][1000 genomes]
rs3108542	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108543	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108544	0.95[EUR][1000 genomes]
rs3108545	0.94[EUR][1000 genomes]
rs3108546	0.92[EUR][1000 genomes]
rs3108550	0.94[EUR][1000 genomes]
rs3108552	0.94[EUR][1000 genomes]
rs3108555	0.88[EUR][1000 genomes]
rs3108559	0.88[EUR][1000 genomes]
rs3108560	0.88[EUR][1000 genomes]
rs3108562	0.88[EUR][1000 genomes]
rs3108563	0.88[EUR][1000 genomes]
rs3108564	0.88[EUR][1000 genomes]
rs3108565	0.83[EUR][1000 genomes]
rs3108566	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108567	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108568	0.85[EUR][1000 genomes]
rs3108570	0.85[EUR][1000 genomes]
rs3108572	0.85[EUR][1000 genomes]
rs3108574	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108575	0.85[EUR][1000 genomes]
rs3108576	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108577	0.85[EUR][1000 genomes]
rs3108579	0.85[EUR][1000 genomes]
rs3108580	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108594	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108596	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108597	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108598	0.86[ASN][1000 genomes]
rs3108600	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108602	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108603	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108607	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108608	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3108609	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108610	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3111541	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111542	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111547	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3111550	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34002069	0.94[EUR][1000 genomes]
rs34395293	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4572520	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4806336	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7245414	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7248477	0.94[EUR][1000 genomes]
rs7252957	0.82[EUR][1000 genomes]
rs7259195	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7259256	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8105197	0.83[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3111549	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs3111549	AC092295.7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:92 , 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	chr19:37098000-37104600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:37098000-37106200	Strong transcription	Brain Hippocampus Middle	brain
19	chr19:37098000-37118200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:37098200-37108400	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr19:37098200-37120400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:37098400-37104000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:37098400-37105000	ZNF genes & repeats	Liver	Liver
25	chr19:37098400-37107400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:37098600-37104000	Strong transcription	Brain Anterior Caudate	brain
27	chr19:37098600-37104000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:37098600-37105200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr19:37098600-37105600	Strong transcription	Brain Angular Gyrus	brain
30	chr19:37098600-37106200	Strong transcription	Ovary	ovary
31	chr19:37098800-37104000	Strong transcription	Brain Germinal Matrix	brain
32	chr19:37098800-37105000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:37098800-37106000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:37098800-37108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:37099000-37105600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:37099000-37109200	Strong transcription	Dnd41	blood
37	chr19:37099200-37105800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:37099200-37110000	Strong transcription	Brain Cingulate Gyrus	brain
39	chr19:37099600-37105800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:37099600-37108400	Strong transcription	Fetal Muscle Leg	muscle
41	chr19:37100200-37107600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:37100800-37105000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:37101000-37104200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr19:37101000-37107000	Weak transcription	Aorta	Aorta
45	chr19:37101000-37107000	Weak transcription	Pancreas	Pancrea
46	chr19:37101000-37107000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:37101400-37112800	Weak transcription	Osteobl	bone
48	chr19:37101800-37111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:37102000-37105200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:37102000-37105600	Weak transcription	Left Ventricle	heart

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