Variant report

Variant	rs58158474
Chromosome Location	chr12:122440027-122440028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122437989..122441020-chr12:122459413..122461657,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11043275	0.85[ASN][1000 genomes]
rs1824949	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1851597	0.87[AMR][1000 genomes]
rs2004863	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2004864	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2076860	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272132	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3741581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522209	0.80[EUR][1000 genomes]
rs55778445	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57298119	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58025403	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58026220	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58516770	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58642707	0.87[EUR][1000 genomes]
rs59116149	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59178789	1.00[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	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6486793	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7138299	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7138556	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7294535	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7294829	1.00[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	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs830125	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs872781	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884785	0.84[EUR][1000 genomes]
rs884786	0.93[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
rs58158474	BCL7A	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122422800-122442600	Weak transcription	Fetal Kidney	kidney
2	chr12:122430400-122441000	Weak transcription	HSMMtube	muscle
3	chr12:122430400-122441600	Weak transcription	Primary T cells from cord blood	blood
4	chr12:122431000-122442000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:122435000-122440600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:122435200-122441200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:122435200-122441600	Weak transcription	Osteobl	bone
8	chr12:122435200-122442400	Weak transcription	Pancreas	Pancrea
9	chr12:122435400-122440600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:122435400-122441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:122435800-122441000	Weak transcription	Primary B cells from cord blood	blood
12	chr12:122438000-122441400	Weak transcription	NHLF	lung
13	chr12:122438000-122444400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:122438200-122441600	Weak transcription	Spleen	Spleen
15	chr12:122438600-122443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:122438800-122440800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:122439400-122441200	Enhancers	Brain Cingulate Gyrus	brain
18	chr12:122439400-122441600	Enhancers	Dnd41	blood
19	chr12:122439400-122443200	Enhancers	Brain Substantia Nigra	brain
20	chr12:122439600-122440600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:122439600-122441400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:122439800-122440400	Weak transcription	Brain Anterior Caudate	brain
23	chr12:122439800-122440600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:122439800-122441000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:122439800-122441800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:122439800-122441800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:122439800-122445200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:122440000-122440400	Weak transcription	Thymus	Thymus
29	chr12:122440000-122440600	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:122440000-122441000	Weak transcription	NHEK	skin
31	chr12:122440000-122441600	Enhancers	Fetal Thymus	thymus
32	chr12:122440000-122441800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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