Variant report

Variant	rs56301546
Chromosome Location	chr19:56910733-56910734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56902006..56908060-chr19:56909612..56917978,15	K562	blood:

Variant related genes	Relation type
ENSG00000266631	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000267454	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10432288	0.83[EUR][1000 genomes]
rs11084446	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11084449	0.83[EUR][1000 genomes]
rs11084450	0.85[EUR][1000 genomes]
rs11667815	0.82[EUR][1000 genomes]
rs12460342	0.85[EUR][1000 genomes]
rs12608966	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12609819	0.84[EUR][1000 genomes]
rs12610115	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12973407	0.86[EUR][1000 genomes]
rs12981146	0.82[EUR][1000 genomes]
rs12981443	0.86[EUR][1000 genomes]
rs2288860	0.90[EUR][1000 genomes]
rs28373215	0.84[EUR][1000 genomes]
rs2904016	0.90[EUR][1000 genomes]
rs2904017	0.85[EUR][1000 genomes]
rs3745826	0.82[EUR][1000 genomes]
rs3760849	0.84[EUR][1000 genomes]
rs3810340	0.86[EUR][1000 genomes]
rs4281830	0.85[EUR][1000 genomes]
rs4801319	0.84[EUR][1000 genomes]
rs55874363	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59858465	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248278	0.85[EUR][1000 genomes]
rs7252607	0.86[EUR][1000 genomes]
rs7258010	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728232	0.85[EUR][1000 genomes]
rs8102580	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8104319	0.85[EUR][1000 genomes]
rs8104585	0.85[EUR][1000 genomes]
rs8112531	0.80[EUR][1000 genomes]
rs8112935	0.80[EUR][1000 genomes]
rs917650	0.85[EUR][1000 genomes]
rs917651	0.85[EUR][1000 genomes]
rs917652	0.85[EUR][1000 genomes]
rs9749140	0.85[EUR][1000 genomes]
rs9789281	0.86[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	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active 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	88 gene(s)	inside rSNPs	diseases
7	nsv544096	chr19:56905651-56933455	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs56301546	ZNF582-AS1	cis	Artery Tibial	GTEx
rs56301546	ZNF582-AS1	cis	Adipose Subcutaneous	GTEx
rs56301546	ZNF582-AS1	cis	lung	GTEx
rs56301546	ZNF582-AS1	cis	Thyroid	GTEx
rs56301546	ZNF582-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56905000-56913600	ZNF genes & repeats	Liver	Liver
2	chr19:56905400-56910800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:56905400-56911000	Weak transcription	Stomach Mucosa	stomach
4	chr19:56905600-56914600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:56905800-56914400	Weak transcription	Fetal Heart	heart
6	chr19:56908000-56913600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:56908000-56913600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr19:56908000-56914800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:56908200-56911400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:56908200-56912400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr19:56908200-56913000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr19:56908200-56914600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:56908400-56911800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr19:56908400-56912000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:56908400-56912000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr19:56908400-56913600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:56908600-56911000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:56908600-56911600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
19	chr19:56908600-56912200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:56908600-56913400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
21	chr19:56908800-56911200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
22	chr19:56908800-56911200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
23	chr19:56908800-56911400	ZNF genes & repeats	Primary T cells from cord blood	blood
24	chr19:56908800-56911600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:56908800-56911600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:56908800-56911600	Strong transcription	Brain Cingulate Gyrus	brain
27	chr19:56908800-56911600	Strong transcription	Brain Hippocampus Middle	brain
28	chr19:56908800-56912000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:56908800-56912000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:56908800-56913600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr19:56908800-56913600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
32	chr19:56909000-56910800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr19:56909000-56911000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:56909000-56911000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr19:56909000-56911000	ZNF genes & repeats	Spleen	Spleen
36	chr19:56909000-56911200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:56909000-56911200	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr19:56909000-56911200	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr19:56909000-56911400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:56909000-56911400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
41	chr19:56909000-56911600	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr19:56909000-56911800	Strong transcription	Left Ventricle	heart
43	chr19:56909000-56912000	ZNF genes & repeats	Fetal Stomach	stomach
44	chr19:56909000-56912000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
45	chr19:56909000-56913600	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr19:56909200-56910800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:56909200-56911000	ZNF genes & repeats	Ovary	ovary
48	chr19:56909200-56911400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr19:56909200-56911400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:56909200-56911600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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