Variant report

Variant	rs2076860
Chromosome Location	chr12:122435142-122435143
allele	C/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	MAFK	chr12:122435087-122435438	IMR90	lung:	n/a	chr12:122435256-122435271
2	FOS	chr12:122435138-122435460	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr12:122435100-122435250	GM12872	blood:	n/a	n/a
4	MAFK	chr12:122435113-122435321	HepG2	liver:	n/a	chr12:122435256-122435271
5	MAFK	chr12:122435114-122435314	K562	blood:	n/a	chr12:122435256-122435271
6	FOS	chr12:122435109-122435448	MCF10A-Er-Src	breast:	n/a	n/a
7	MAFK	chr12:122435108-122435396	Hela-S3	cervix:	n/a	chr12:122435256-122435271
8	FOSL2	chr12:122434926-122435604	SK-N-SH	brain:	n/a	n/a
9	FOS	chr12:122435109-122435420	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
WDR66	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11043275	0.85[ASN][1000 genomes]
rs1824949	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2004863	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2004864	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2272132	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3741581	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522209	1.00[ASW][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs55778445	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57298119	0.97[EUR][1000 genomes]
rs58025403	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58026220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58158474	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58516770	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58642707	0.87[EUR][1000 genomes]
rs59116149	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59178789	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695002	0.87[EUR][1000 genomes]
rs60620185	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6486792	0.97[EUR][1000 genomes]
rs6486793	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7138299	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7138556	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7294535	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7294829	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303779	0.93[EUR][1000 genomes]
rs7314352	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7964151	0.97[EUR][1000 genomes]
rs830125	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs872781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884785	0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs884786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2076860	RBM46	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
2	chr12:122418800-122437600	Weak transcription	Spleen	Spleen
3	chr12:122422800-122442600	Weak transcription	Fetal Kidney	kidney
4	chr12:122430400-122441000	Weak transcription	HSMMtube	muscle
5	chr12:122430400-122441600	Weak transcription	Primary T cells from cord blood	blood
6	chr12:122430800-122438800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:122431000-122442000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:122433000-122435200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:122433000-122435200	Enhancers	HepG2	liver
10	chr12:122433200-122438600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:122433400-122435400	Enhancers	Thymus	Thymus
12	chr12:122433400-122436200	Enhancers	Fetal Thymus	thymus
13	chr12:122433600-122435200	Enhancers	Primary hematopoietic stem cells	blood
14	chr12:122433600-122435200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:122433600-122436000	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:122433800-122435200	Enhancers	NHLF	lung
17	chr12:122433800-122435400	Enhancers	Fetal Heart	heart
18	chr12:122433800-122435800	Enhancers	Primary B cells from cord blood	blood
19	chr12:122434000-122435200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:122434000-122435200	Enhancers	Aorta	Aorta
21	chr12:122434200-122435200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:122434200-122435200	Enhancers	Osteobl	bone
23	chr12:122434600-122435200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:122434600-122435200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr12:122434600-122435200	Enhancers	Brain Hippocampus Middle	brain
26	chr12:122434600-122435200	Enhancers	K562	blood
27	chr12:122434600-122435400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:122434600-122435400	Enhancers	NHDF-Ad	bronchial
29	chr12:122434800-122435200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:122434800-122435200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:122434800-122435200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:122434800-122435200	Enhancers	Left Ventricle	heart
33	chr12:122434800-122435200	Enhancers	Pancreas	Pancrea
34	chr12:122434800-122435200	Enhancers	A549	lung
35	chr12:122434800-122435400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:122434800-122435400	Enhancers	HMEC	breast
37	chr12:122434800-122436000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:122435000-122435200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:122435000-122435400	Enhancers	NHEK	skin
40	chr12:122435000-122440600	Weak transcription	Brain Inferior Temporal Lobe	brain

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