Variant report

Variant	rs2899057
Chromosome Location	chr15:42812793-42812794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42808288..42811039-chr15:42812742..42814723,2	K562	blood:
2	chr15:42812167..42816411-chr15:42819043..42822094,4	K562	blood:
3	chr15:42802805..42805415-chr15:42810505..42813373,2	K562	blood:
4	chr15:42803044..42805415-chr15:42811616..42813373,2	K562	blood:

Variant related genes	Relation type
ENSG00000092531	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10454039	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1060291	0.89[EUR][1000 genomes]
rs10851410	0.82[EUR][1000 genomes]
rs10851411	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11022	0.89[EUR][1000 genomes]
rs11070374	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11631193	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638208	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12324113	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12324717	0.83[EUR][1000 genomes]
rs12903432	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906697	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913324	0.83[EUR][1000 genomes]
rs1900921	0.89[EUR][1000 genomes]
rs2241998	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2255995	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2595939	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2595940	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2595941	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617236	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28886308	0.85[EUR][1000 genomes]
rs2899051	0.86[EUR][1000 genomes]
rs34643746	0.83[EUR][1000 genomes]
rs3986280	0.83[EUR][1000 genomes]
rs4573906	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923947	0.92[ASN][1000 genomes]
rs4923948	0.88[EUR][1000 genomes]
rs4924684	0.89[EUR][1000 genomes]
rs56357092	0.89[EUR][1000 genomes]
rs60380503	0.85[EUR][1000 genomes]
rs7169615	0.80[EUR][1000 genomes]
rs8033412	0.89[EUR][1000 genomes]
rs9302112	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2899057	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs2899057	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42790800-42821400	Weak transcription	Right Ventricle	heart
2	chr15:42793000-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:42793800-42837200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:42797600-42822200	Weak transcription	Small Intestine	intestine
6	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
8	chr15:42802400-42839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42802600-42817400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr15:42802800-42817200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:42803200-42837200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:42803600-42839400	Weak transcription	A549	lung
13	chr15:42803800-42817600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:42804000-42826800	Strong transcription	HUVEC	blood vessel
15	chr15:42804400-42814400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:42804600-42836400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:42804800-42814600	Strong transcription	Primary T cells from cord blood	blood
18	chr15:42804800-42817200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:42804800-42817400	Strong transcription	Adipose Nuclei	Adipose
20	chr15:42804800-42818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:42804800-42818000	Strong transcription	Fetal Intestine Large	intestine
22	chr15:42804800-42825400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:42804800-42828800	Strong transcription	Placenta	Placenta
24	chr15:42804800-42836400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:42804800-42836400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:42805000-42814400	Strong transcription	Fetal Thymus	thymus
27	chr15:42805000-42814600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:42805000-42818400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr15:42805000-42818800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:42805000-42818800	Strong transcription	NH-A	brain
31	chr15:42805200-42814200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr15:42805200-42817000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:42805200-42817600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:42805200-42825800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:42805400-42813600	Strong transcription	Fetal Muscle Leg	muscle
36	chr15:42805400-42814600	Strong transcription	Liver	Liver
37	chr15:42805400-42816600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:42805400-42816600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:42805400-42836800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:42805600-42814400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:42805600-42818400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:42805600-42818800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:42805800-42814000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:42806200-42836400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:42806200-42839000	Weak transcription	Fetal Brain Male	brain
46	chr15:42807200-42816600	Weak transcription	Pancreas	Pancrea
47	chr15:42807600-42813000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:42807600-42821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:42808200-42820400	Weak transcription	Brain Angular Gyrus	brain
50	chr15:42808200-42824800	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links