Variant report

Variant	rs11920390
Chromosome Location	chr3:111056828-111056829
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111056650..111057560-chr6:35896614..35897332,2	MCF-7	breast:
2	chr3:110731069..110732115-chr3:111056580..111057412,8	MCF-7	breast:
3	chr3:110731260..110732165-chr3:111056692..111057428,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10511294	0.89[ASN][1000 genomes]
rs11920391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12106997	0.89[ASN][1000 genomes]
rs1489030	0.89[ASN][1000 genomes]
rs1489031	0.89[ASN][1000 genomes]
rs1489032	0.91[ASN][1000 genomes]
rs1489033	1.00[ASN][1000 genomes]
rs1489034	1.00[ASN][1000 genomes]
rs1489035	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634552	0.89[ASN][1000 genomes]
rs2634553	0.89[ASN][1000 genomes]
rs2634554	0.89[ASN][1000 genomes]
rs2675587	0.89[ASN][1000 genomes]
rs28831219	0.97[ASN][1000 genomes]
rs28846108	0.97[ASN][1000 genomes]
rs2932047	0.89[ASN][1000 genomes]
rs2932071	0.89[ASN][1000 genomes]
rs2932074	0.85[ASN][1000 genomes]
rs2950971	0.86[ASN][1000 genomes]
rs2958079	0.91[ASN][1000 genomes]
rs2958080	0.89[ASN][1000 genomes]
rs2971363	0.89[ASN][1000 genomes]
rs2971364	0.89[ASN][1000 genomes]
rs2971365	0.89[ASN][1000 genomes]
rs2971366	0.89[ASN][1000 genomes]
rs4145124	0.89[ASN][1000 genomes]
rs6808323	0.97[ASN][1000 genomes]
rs7620684	0.97[ASN][1000 genomes]
rs7621095	0.97[ASN][1000 genomes]
rs7624812	1.00[ASN][1000 genomes]
rs7636637	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837511	0.94[ASN][1000 genomes]
rs9854335	1.00[ASN][1000 genomes]
rs9868323	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878888	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11920390	PHLDB2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111053200-111060800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:111054400-111057400	Enhancers	Fetal Thymus	thymus
3	chr3:111054800-111057000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:111054800-111057200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:111055000-111057200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:111055800-111057000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:111055800-111057200	Weak transcription	HSMM	muscle
8	chr3:111056000-111057000	Weak transcription	Primary T cells from cord blood	blood
9	chr3:111056200-111057000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:111056200-111060000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:111056400-111057800	Enhancers	Dnd41	blood
12	chr3:111056800-111057000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:111056800-111057000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:111056800-111057000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:111056800-111057000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:111056800-111057000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:111056800-111057400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:111056800-111057400	Enhancers	HMEC	breast
19	chr3:111056800-111057400	Enhancers	Osteobl	bone

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