Variant report

Variant	rs4238572
Chromosome Location	chr15:34538560-34538561
allele	G/T
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	chr15:34538305-34538753	A549	lung:	n/a	chr15:34538486-34538495 chr15:34538485-34538496 chr15:34538486-34538495
2	CEBPB	chr15:34538356-34538779	HepG2	liver:	n/a	chr15:34538486-34538495 chr15:34538485-34538496 chr15:34538486-34538495
3	CEBPB	chr15:34538339-34538822	IMR90	lung:	n/a	chr15:34538486-34538495 chr15:34538485-34538496 chr15:34538486-34538495
4	CEBPB	chr15:34538477-34538848	K562	blood:	n/a	chr15:34538486-34538495 chr15:34538485-34538496 chr15:34538486-34538495
5	CEBPB	chr15:34538478-34538781	Hela-S3	cervix:	n/a	chr15:34538486-34538495 chr15:34538485-34538496 chr15:34538486-34538495

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34536523..34539176-chr15:34546816..34548491,2	K562	blood:
2	chr15:34516970..34518662-chr15:34536000..34538660,2	K562	blood:

Variant related genes	Relation type
SLC12A6	TF binding region
ENSG00000128463	Chromatin interaction
ENSG00000259468	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1045204	0.88[GIH][hapmap]
rs10851964	0.81[CHD][hapmap]
rs1133154	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12050753	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12591967	0.90[GIH][hapmap]
rs12595504	0.87[GIH][hapmap]
rs16958878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958954	0.91[GIH][hapmap];0.81[LWK][hapmap]
rs16959021	0.91[GIH][hapmap]
rs17236763	0.92[ASN][1000 genomes]
rs17236777	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs17236784	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs17236798	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17236819	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17817800	0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17817806	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs180886	0.91[GIH][hapmap]
rs2244040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs2290940	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2290941	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2290942	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2705343	1.00[ASW][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs4530104	0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs4780231	0.85[CHB][hapmap]
rs4780233	0.92[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4780234	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56761496	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57494441	0.91[ASN][1000 genomes]
rs57626952	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59023791	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59091709	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59209438	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59712831	0.91[ASN][1000 genomes]
rs60165224	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs60604568	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61549125	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495639	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495646	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs6495662	0.84[GIH][hapmap]
rs7168761	0.83[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap]
rs7175028	0.91[GIH][hapmap]
rs7178002	0.82[CHD][hapmap]
rs73386033	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73386037	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73386038	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73388003	0.91[ASN][1000 genomes]
rs73388020	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73388027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73388046	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73388049	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8025057	0.88[GIH][hapmap]
rs8031145	0.91[GIH][hapmap]
rs8031147	0.91[GIH][hapmap]
rs8031404	0.87[GIH][hapmap]
rs8032347	0.82[GIH][hapmap]
rs8035954	0.84[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs8036468	0.83[CHD][hapmap]
rs8040071	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4238572	NOP10	cis	Esophagus Muscularis	GTEx
rs4238572	SLC12A6	cis	Thyroid	GTEx
rs4238572	NOP10	cis	Artery Tibial	GTEx
rs4238572	NOP10	cis	Esophagus Mucosa	GTEx
rs4238572	NOP10	cis	Thyroid	GTEx
rs4238572	TMEM85	cis	cerebellum	SCAN
rs4238572	NOP10	cis	Heart Left Ventricle	GTEx
rs4238572	TMEM85	cis	parietal	SCAN
rs4238572	NOP10	cis	Muscle Skeletal	GTEx
rs4238572	NOP10	cis	parietal	SCAN
rs4238572	NOP10	cis	Skin Sun Exposed Lower leg	GTEx
rs4238572	NOP10	cis	cerebellum	SCAN
rs4238572	NOP10	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34518000-34571800	Weak transcription	Stomach Mucosa	stomach
2	chr15:34518800-34548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:34519000-34552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:34519200-34552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:34519200-34553600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:34519400-34540800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:34519400-34552200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:34519400-34552200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:34519600-34544200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:34519600-34553600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:34519800-34540000	Strong transcription	Liver	Liver
12	chr15:34519800-34544800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:34520200-34555600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:34521000-34547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:34523000-34545600	Weak transcription	Dnd41	blood
16	chr15:34524200-34552400	Strong transcription	Primary B cells from cord blood	blood
17	chr15:34524800-34553600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr15:34525200-34540400	Strong transcription	Primary T cells from cord blood	blood
19	chr15:34528400-34546400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:34528400-34547400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:34528600-34554600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:34529000-34543800	Weak transcription	Right Ventricle	heart
23	chr15:34529000-34554800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:34529200-34542800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:34529200-34544000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:34529200-34546000	Weak transcription	Gastric	stomach
27	chr15:34529200-34550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:34529200-34552200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:34529800-34542600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:34529800-34544000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:34529800-34546200	Weak transcription	Esophagus	oesophagus
32	chr15:34530800-34541600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:34531400-34540800	Weak transcription	Psoas Muscle	Psoas
34	chr15:34531400-34541000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:34531400-34542200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:34531400-34546000	Weak transcription	Spleen	Spleen
37	chr15:34531400-34546400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:34532000-34546000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:34532600-34540200	Weak transcription	A549	lung
40	chr15:34532600-34542000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:34532600-34543800	Weak transcription	HSMM	muscle
42	chr15:34533000-34544200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:34533000-34545800	Weak transcription	Hela-S3	cervix
44	chr15:34533000-34548400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:34533000-34555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:34533000-34556600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:34533000-34564000	Weak transcription	NHLF	lung
48	chr15:34533200-34538800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:34533200-34539200	Strong transcription	GM12878-XiMat	blood
50	chr15:34533200-34541000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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