Variant report

Variant	rs2239189
Chromosome Location	chr12:48146590-48146591
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	MAFK	chr12:48146272-48146607	IMR90	lung:	n/a	n/a
2	EP300	chr12:48146238-48148408	SK-N-SH	brain:	n/a	chr12:48147400-48147414
3	STAT3	chr12:48146319-48146735	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
4	MAFK	chr12:48146336-48146678	Hela-S3	cervix:	n/a	n/a
5	MAX	chr12:48146353-48146702	Hela-S3	cervix:	n/a	n/a
6	FOS	chr12:48146293-48146766	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:48146404-48146706	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:48146475-48146676	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr12:48146292-48146727	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr12:48146321-48146736	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
11	STAT3	chr12:48146420-48146738	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
12	FOS	chr12:48146309-48146738	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr12:48146293-48146735	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr12:48146410-48146651	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr12:48146302-48146819	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
16	FOS	chr12:48146300-48146699	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr12:48146291-48146697	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr12:48146426-48148248	Hela-S3	cervix:	n/a	n/a
19	SMARCC1	chr12:48146110-48149011	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:48146395-48149013	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr12:48146320-48146616	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48139218..48143283-chr12:48146093..48149337,5	K562	blood:
2	chr12:48146163..48148373-chr12:48150555..48153521,2	K562	blood:
3	chr12:48145973..48147793-chr12:48165632..48167203,2	MCF-7	breast:
4	chr12:48146517..48147373-chr19:1173092..1174043,2	Hela-S3	cervix:
5	chr12:48108739..48111513-chr12:48143992..48146721,2	MCF-7	breast:
6	chr12:48145090..48147406-chr12:48155481..48157824,2	K562	blood:
7	chr12:48144826..48150380-chr12:48164026..48173211,11	K562	blood:
8	chr12:48144391..48147829-chr12:48212557..48216683,4	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
SLC48A1	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000064932	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1018939	1.00[ASN][1000 genomes]
rs10875690	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11168224	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11168228	0.82[CHD][hapmap]
rs1548518	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs7397928	0.89[CHD][hapmap]
rs757286	0.99[ASN][1000 genomes]
rs757287	1.00[ASN][1000 genomes]
rs7963444	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2239189	ENDOU	cis	parietal	SCAN
rs2239189	RAPGEF3	cis	parietal	SCAN
rs2239189	TMEM117	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
5	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
6	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:48138000-48148000	Weak transcription	Liver	Liver
10	chr12:48138400-48146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:48139400-48147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:48139800-48146600	Weak transcription	Fetal Lung	lung
13	chr12:48139800-48146800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:48140200-48146800	Weak transcription	Fetal Heart	heart
15	chr12:48141200-48147600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:48141600-48147000	Weak transcription	GM12878-XiMat	blood
17	chr12:48141800-48147000	Weak transcription	Primary B cells from cord blood	blood
18	chr12:48143200-48147000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:48143800-48146600	Weak transcription	Aorta	Aorta
20	chr12:48144200-48146800	Enhancers	HMEC	breast
21	chr12:48144200-48150000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:48144200-48150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:48144200-48151000	Weak transcription	Brain Germinal Matrix	brain
24	chr12:48144800-48146800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:48144800-48147400	Weak transcription	Fetal Kidney	kidney
26	chr12:48145000-48149000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:48145200-48146600	Enhancers	Hela-S3	cervix
28	chr12:48145200-48146800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr12:48145200-48147000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr12:48145200-48148600	Genic enhancers	Brain Hippocampus Middle	brain
31	chr12:48145200-48148600	Enhancers	Esophagus	oesophagus
32	chr12:48145200-48149000	Enhancers	HSMM	muscle
33	chr12:48145400-48147200	Weak transcription	Pancreas	Pancrea
34	chr12:48145400-48148400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr12:48145400-48148400	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr12:48145400-48148800	Enhancers	Left Ventricle	heart
37	chr12:48145400-48150800	Enhancers	NHDF-Ad	bronchial
38	chr12:48145400-48151400	Enhancers	Placenta	Placenta
39	chr12:48145600-48146600	Enhancers	Adipose Nuclei	Adipose
40	chr12:48145600-48147800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:48145600-48147800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr12:48145600-48148400	Enhancers	A549	lung
43	chr12:48145600-48149600	Enhancers	Lung	lung
44	chr12:48145600-48149800	Enhancers	HSMMtube	muscle
45	chr12:48145600-48150000	Enhancers	Fetal Muscle Trunk	muscle
46	chr12:48145600-48150200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr12:48145600-48150800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr12:48145600-48151000	Enhancers	Spleen	Spleen
49	chr12:48145800-48147400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr12:48145800-48147400	Enhancers	Stomach Smooth Muscle	stomach

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