Variant report

Variant	rs12610115
Chromosome Location	chr19:56915855-56915856
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	chr19:56902006..56908060-chr19:56909612..56917978,15	K562	blood:
2	chr19:56902257..56906485-chr19:56913118..56917978,7	K562	blood:

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

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10408604	0.80[EUR][1000 genomes]
rs10415307	0.80[EUR][1000 genomes]
rs10416345	0.80[EUR][1000 genomes]
rs10419332	0.80[EUR][1000 genomes]
rs10432288	0.85[EUR][1000 genomes]
rs11084446	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11084449	0.85[EUR][1000 genomes]
rs11084450	0.87[EUR][1000 genomes]
rs11667815	0.84[EUR][1000 genomes]
rs12460342	0.87[EUR][1000 genomes]
rs12608966	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12609819	0.86[EUR][1000 genomes]
rs12973407	0.88[EUR][1000 genomes]
rs12981146	0.84[EUR][1000 genomes]
rs12981443	0.88[EUR][1000 genomes]
rs2288860	0.89[EUR][1000 genomes]
rs28373215	0.86[EUR][1000 genomes]
rs2904016	0.89[EUR][1000 genomes]
rs2904017	0.87[EUR][1000 genomes]
rs35914474	0.82[EUR][1000 genomes]
rs3745826	0.84[EUR][1000 genomes]
rs3760849	0.86[EUR][1000 genomes]
rs3810340	0.88[EUR][1000 genomes]
rs4281830	0.87[EUR][1000 genomes]
rs4801319	0.86[EUR][1000 genomes]
rs55874363	0.82[EUR][1000 genomes]
rs56301546	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59858465	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121590	0.82[EUR][1000 genomes]
rs62121593	0.80[EUR][1000 genomes]
rs7248278	0.87[EUR][1000 genomes]
rs7252607	0.88[EUR][1000 genomes]
rs7258010	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs728232	0.87[EUR][1000 genomes]
rs8102580	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8104319	0.87[EUR][1000 genomes]
rs8104585	0.87[EUR][1000 genomes]
rs8112531	0.82[EUR][1000 genomes]
rs8112935	0.82[EUR][1000 genomes]
rs917650	0.87[EUR][1000 genomes]
rs917651	0.87[EUR][1000 genomes]
rs917652	0.87[EUR][1000 genomes]
rs9749140	0.87[EUR][1000 genomes]
rs9789281	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	esv3373403	chr19:56913940-56918638	Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3389334	chr19:56914840-56917838	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12610115	ZNF582-AS1	cis	Esophagus Muscularis	GTEx
rs12610115	ZNF582-AS1	cis	lung	GTEx
rs12610115	ZNF582-AS1	cis	Artery Tibial	GTEx
rs12610115	ZNF582-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56914200-56916000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:56914200-56916000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr19:56914200-56916000	Active TSS	HSMMtube	muscle
4	chr19:56914200-56916000	Active TSS	NHDF-Ad	bronchial
5	chr19:56914200-56916200	Active TSS	Muscle Satellite Cultured Cells	--
6	chr19:56914400-56916000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr19:56914400-56916000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr19:56914400-56916000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:56914400-56916000	Active TSS	Brain Cingulate Gyrus	brain
10	chr19:56914400-56916000	Active TSS	Fetal Brain Female	brain
11	chr19:56914400-56916000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:56914400-56916000	Active TSS	NHLF	lung
13	chr19:56914400-56916200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:56914400-56916400	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr19:56914400-56916800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:56914600-56916000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:56914600-56916000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:56914600-56916000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr19:56914600-56916000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:56914600-56916000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:56914600-56916000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:56914600-56916000	Active TSS	Colonic Mucosa	Colon
23	chr19:56914600-56916000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr19:56914600-56916000	Active TSS	Gastric	stomach
25	chr19:56914600-56916000	Active TSS	NH-A	brain
26	chr19:56914600-56916200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr19:56914600-56916200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:56914600-56916200	Active TSS	Fetal Intestine Large	intestine
29	chr19:56914600-56916400	Active TSS	Psoas Muscle	Psoas
30	chr19:56914600-56916800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr19:56914600-56916800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:56914600-56917600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:56914800-56916000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:56914800-56916000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:56914800-56916000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:56914800-56916000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:56914800-56916000	Active TSS	Brain Anterior Caudate	brain
38	chr19:56914800-56916000	Active TSS	Brain Hippocampus Middle	brain
39	chr19:56914800-56916000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:56914800-56916000	Active TSS	Fetal Lung	lung
41	chr19:56914800-56916000	Active TSS	Left Ventricle	heart
42	chr19:56914800-56916000	Active TSS	Ovary	ovary
43	chr19:56914800-56916000	Active TSS	Placenta Amnion	Placenta Amnion
44	chr19:56914800-56916000	Active TSS	Right Ventricle	heart
45	chr19:56914800-56916000	Active TSS	GM12878-XiMat	blood
46	chr19:56914800-56916200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:56914800-56916200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:56914800-56916200	Active TSS	Fetal Intestine Small	intestine
49	chr19:56914800-56916200	Active TSS	Stomach Mucosa	stomach
50	chr19:56915000-56916000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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