Variant report

Variant	rs56357092
Chromosome Location	chr15:42790529-42790530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42781216..42785618-chr15:42786050..42793334,15	K562	blood:
2	chr15:42786351..42790033-chr15:42790160..42794805,5	K562	blood:
3	chr15:42782381..42786334-chr15:42789829..42792638,5	K562	blood:

Variant related genes	Relation type
ENSG00000103994	Chromatin interaction
ENSG00000092531	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10454039	0.90[EUR][1000 genomes]
rs10518766	1.00[ASN][1000 genomes]
rs1060291	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060293	1.00[ASN][1000 genomes]
rs10851410	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10851411	0.88[EUR][1000 genomes]
rs11022	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070374	0.89[EUR][1000 genomes]
rs11070376	1.00[ASN][1000 genomes]
rs11631193	0.88[EUR][1000 genomes]
rs11636577	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638208	0.86[EUR][1000 genomes]
rs12324113	0.93[EUR][1000 genomes]
rs12324717	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12903432	0.95[EUR][1000 genomes]
rs12906697	0.90[EUR][1000 genomes]
rs12913324	0.82[EUR][1000 genomes]
rs16973320	1.00[ASN][1000 genomes]
rs17709180	1.00[ASN][1000 genomes]
rs17709377	1.00[ASN][1000 genomes]
rs17766532	1.00[ASN][1000 genomes]
rs1900921	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241998	0.88[EUR][1000 genomes]
rs2255995	0.95[EUR][1000 genomes]
rs2595939	0.95[EUR][1000 genomes]
rs2595940	0.95[EUR][1000 genomes]
rs2595941	0.94[EUR][1000 genomes]
rs2617236	0.92[EUR][1000 genomes]
rs28886308	0.84[EUR][1000 genomes]
rs2899051	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899057	0.89[EUR][1000 genomes]
rs34359922	1.00[ASN][1000 genomes]
rs34643746	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792942	1.00[ASN][1000 genomes]
rs3986280	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4573906	0.95[EUR][1000 genomes]
rs4923948	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924684	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924687	1.00[ASN][1000 genomes]
rs56982416	1.00[ASN][1000 genomes]
rs58042601	1.00[ASN][1000 genomes]
rs58641431	1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	1.00[ASN][1000 genomes]
rs60380503	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60584955	1.00[ASN][1000 genomes]
rs60812675	1.00[ASN][1000 genomes]
rs61489160	1.00[ASN][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7180483	1.00[ASN][1000 genomes]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	1.00[ASN][1000 genomes]
rs73404723	1.00[ASN][1000 genomes]
rs73404730	1.00[ASN][1000 genomes]
rs73404763	1.00[ASN][1000 genomes]
rs73406518	1.00[ASN][1000 genomes]
rs73406534	1.00[ASN][1000 genomes]
rs73406545	1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302112	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56357092	CEP27	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42788400-42808000	Weak transcription	Esophagus	oesophagus
2	chr15:42788600-42790600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:42788600-42790800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:42788600-42791000	Enhancers	Primary B cells from peripheral blood	blood
5	chr15:42788600-42791400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:42788600-42792400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr15:42788600-42798400	Weak transcription	Ovary	ovary
8	chr15:42788600-42805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:42788600-42806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:42788600-42807200	Weak transcription	Fetal Kidney	kidney
11	chr15:42788800-42790600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:42788800-42790600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:42788800-42790600	Weak transcription	HMEC	breast
14	chr15:42788800-42790800	Weak transcription	NHDF-Ad	bronchial
15	chr15:42788800-42791400	Weak transcription	NH-A	brain
16	chr15:42788800-42792000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:42788800-42792200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:42788800-42792200	Weak transcription	Right Atrium	heart
19	chr15:42788800-42792400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:42788800-42793000	Weak transcription	Brain Substantia Nigra	brain
21	chr15:42788800-42793600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:42788800-42797000	Weak transcription	HSMMtube	muscle
23	chr15:42788800-42800400	Weak transcription	Fetal Lung	lung
24	chr15:42788800-42805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:42788800-42805400	Weak transcription	Brain Germinal Matrix	brain
26	chr15:42789000-42790800	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:42789000-42790800	Weak transcription	Osteobl	bone
28	chr15:42789000-42791000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:42789000-42791000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr15:42789000-42791200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:42789000-42791600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:42789000-42791600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:42789000-42791800	Enhancers	Duodenum Mucosa	Duodenum
34	chr15:42789000-42791800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr15:42789000-42792000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:42789000-42792000	Weak transcription	NHLF	lung
37	chr15:42789000-42792200	Weak transcription	Fetal Heart	heart
38	chr15:42789000-42792400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:42789000-42793000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:42789000-42794000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:42789000-42797000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:42789000-42797000	Weak transcription	Brain Angular Gyrus	brain
43	chr15:42789000-42803400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:42789000-42805400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:42789000-42806400	Weak transcription	Thymus	Thymus
46	chr15:42789200-42790600	Enhancers	K562	blood
47	chr15:42789200-42790800	Weak transcription	Stomach Mucosa	stomach
48	chr15:42789200-42791000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:42789200-42791000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:42789200-42791000	Weak transcription	HSMM	muscle

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