Variant report

Variant	rs2139651
Chromosome Location	chr15:43418758-43418759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:43418631-43418906	A549	lung:	n/a	chr15:43418740-43418751
2	CEBPB	chr15:43418679-43418824	HepG2	liver:	n/a	chr15:43418740-43418751
3	CEBPB	chr15:43418595-43418933	HepG2	liver:	n/a	chr15:43418740-43418751
4	CEBPB	chr15:43418636-43418865	K562	blood:	n/a	chr15:43418740-43418751

Variant related genes	Relation type
SPCS2P1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10851414	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070389	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11070390	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629629	0.89[AFR][1000 genomes]
rs11632120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12050604	0.81[ASN][1000 genomes]
rs12442190	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913112	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12913134	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1474200	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs2056346	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2139652	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277532	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs476342	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs489964	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs4923956	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs502157	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs525403	0.86[CHB][hapmap];0.82[MEX][hapmap]
rs530118	0.88[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs531598	0.82[ASN][1000 genomes]
rs574531	0.84[ASN][1000 genomes]
rs574856	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7165861	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7166467	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9635327	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
9	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2139651	LIMA1	trans	lymphoblastoid	seeQTL
rs2139651	VPS39	cis	cerebellum	SCAN
rs2139651	SNAP23	cis	cerebellum	SCAN
rs2139651	TGM5	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43415400-43419200	Weak transcription	Small Intestine	intestine
2	chr15:43415600-43419200	Weak transcription	Pancreas	Pancrea
3	chr15:43415600-43419600	Weak transcription	Stomach Mucosa	stomach
4	chr15:43415600-43425200	Weak transcription	Gastric	stomach
5	chr15:43415800-43419400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:43415800-43419800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:43415800-43419800	Weak transcription	Liver	Liver
8	chr15:43415800-43425000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:43415800-43425000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr15:43415800-43425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:43415800-43425000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:43415800-43425000	Weak transcription	Aorta	Aorta
13	chr15:43415800-43425000	Weak transcription	Brain Anterior Caudate	brain
14	chr15:43415800-43425200	Weak transcription	Esophagus	oesophagus
15	chr15:43416200-43419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:43416200-43419800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:43416200-43419800	Weak transcription	A549	lung
18	chr15:43416200-43425000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:43416800-43419800	Enhancers	Fetal Intestine Large	intestine
20	chr15:43417000-43420600	Enhancers	Fetal Intestine Small	intestine
21	chr15:43417400-43419600	Enhancers	Duodenum Mucosa	Duodenum
22	chr15:43417600-43419800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr15:43417600-43425000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:43417600-43425000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:43417800-43420000	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr15:43418000-43420200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr15:43418000-43422200	Enhancers	HepG2	liver
28	chr15:43418200-43422000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr15:43418400-43425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:43418600-43419600	Weak transcription	Colonic Mucosa	Colon

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