Variant report

Variant	rs2052728
Chromosome Location	chr19:37061565-37061566
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36940091..36943076-chr19:37061156..37065481,3	K562	blood:
2	chr19:37018711..37023188-chr19:37060299..37065354,5	K562	blood:

Variant related genes	Relation type
ENSG00000254004	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000186017	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1035777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10402182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10403456	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10407919	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11084861	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs11667894	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11668432	0.82[ASN][1000 genomes]
rs11668689	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11669816	0.87[ASN][1000 genomes]
rs11670914	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11671382	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11672098	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12608459	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608512	0.83[ASN][1000 genomes]
rs12610555	0.81[ASN][1000 genomes]
rs12610572	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1357879	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464830	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1464831	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1525133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17272386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1985980	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2162296	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2194976	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912399	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912400	0.92[ASN][1000 genomes]
rs2912404	0.89[ASN][1000 genomes]
rs2912408	0.95[ASN][1000 genomes]
rs2912412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912440	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2912442	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2912443	0.98[ASN][1000 genomes]
rs2912444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945964	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945978	0.82[ASN][1000 genomes]
rs2967427	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967429	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2967436	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2967437	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967438	0.95[ASN][1000 genomes]
rs2967439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967440	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967461	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967463	0.94[ASN][1000 genomes]
rs2967464	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967473	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2967545	0.82[ASN][1000 genomes]
rs3096620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3096637	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3108593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35299345	0.82[ASN][1000 genomes]
rs4806338	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4806339	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4806348	0.81[EUR][1000 genomes]
rs4806349	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55940011	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55965207	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60213885	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60297398	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61457535	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6510551	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66717711	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66783290	0.87[ASN][1000 genomes]
rs67258954	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67995015	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68012004	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7246216	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251805	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73609113	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7507224	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs8100381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8108985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826987	0.85[EUR][1000 genomes];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	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2052728	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
2	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
5	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:37025600-37062800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:37028600-37061800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:37034000-37063000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:37048400-37062800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:37049800-37061800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:37050400-37062600	Weak transcription	Fetal Heart	heart
13	chr19:37052800-37063000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:37052800-37063200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:37053400-37063000	Weak transcription	Stomach Mucosa	stomach
16	chr19:37054000-37063200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr19:37054200-37063000	Weak transcription	Osteobl	bone
18	chr19:37054200-37063800	Weak transcription	Gastric	stomach
19	chr19:37054400-37063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:37055200-37061600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
21	chr19:37055400-37061600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:37055600-37061800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:37055600-37062000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:37055600-37062800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:37055600-37063000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr19:37055800-37061800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:37056000-37063400	ZNF genes & repeats	A549	lung
28	chr19:37056200-37061600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:37056200-37061600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:37056200-37062800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:37056200-37063000	Weak transcription	Brain Substantia Nigra	brain
32	chr19:37056400-37063000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:37056600-37061600	Strong transcription	Placenta	Placenta
34	chr19:37057200-37062600	Weak transcription	NHEK	skin
35	chr19:37057200-37062800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:37057200-37063000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:37057400-37061600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:37057400-37063200	Weak transcription	HUVEC	blood vessel
39	chr19:37057600-37062800	Weak transcription	Brain Angular Gyrus	brain
40	chr19:37057800-37062400	ZNF genes & repeats	Fetal Intestine Small	intestine
41	chr19:37058000-37063000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:37058200-37061600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:37058200-37061600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr19:37058400-37062800	Weak transcription	HMEC	breast
45	chr19:37058600-37061800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:37058800-37062400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:37059000-37062600	Weak transcription	HepG2	liver
48	chr19:37059200-37061600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:37059200-37061600	Strong transcription	Brain Anterior Caudate	brain
50	chr19:37059200-37062800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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