Variant report

Variant	rs1282932
Chromosome Location	chr3:111589772-111589773
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111577297..111579661-chr3:111589564..111591815,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10212121	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10804493	0.81[EUR][1000 genomes]
rs10934114	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11711475	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs12490718	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs12695246	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs1282931	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1282970	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs13063024	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13063315	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13083516	0.90[EUR][1000 genomes]
rs13101043	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1913493	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1913494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1913495	0.93[JPT][hapmap]
rs3925080	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs3925081	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs4381907	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs4383483	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs4583615	0.87[EUR][1000 genomes]
rs7626131	0.87[EUR][1000 genomes]
rs7637689	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7638138	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs937553	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs937554	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs967011	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9827362	0.81[EUR][1000 genomes]
rs9846313	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1282932	PHLDB2	cis	lymphoblastoid	seeQTL
rs1282932	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111581400-111593800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:111582200-111593200	Weak transcription	Lung	lung
3	chr3:111583800-111591200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:111584400-111589800	Enhancers	Rectal Smooth Muscle	rectum
5	chr3:111584400-111591000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:111584600-111590800	Weak transcription	Fetal Kidney	kidney
7	chr3:111584600-111591000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:111584600-111593200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
10	chr3:111584800-111591200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:111585200-111591200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:111585200-111591200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:111585200-111591200	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:111585200-111591200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
16	chr3:111585400-111591000	Weak transcription	Ovary	ovary
17	chr3:111585400-111592800	Weak transcription	HSMM	muscle
18	chr3:111585400-111593400	Weak transcription	Psoas Muscle	Psoas
19	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
20	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
21	chr3:111585600-111589800	Enhancers	Stomach Smooth Muscle	stomach
22	chr3:111585600-111591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:111585600-111592400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:111586400-111593000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:111587000-111589800	Genic enhancers	NH-A	brain
26	chr3:111587000-111590200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:111587000-111591200	Weak transcription	Right Atrium	heart
28	chr3:111587000-111591400	Enhancers	Fetal Heart	heart
29	chr3:111587000-111591600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:111587200-111590400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr3:111587200-111590800	Weak transcription	Right Ventricle	heart
32	chr3:111587200-111591000	Weak transcription	Aorta	Aorta
33	chr3:111587200-111593000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:111587200-111593200	Weak transcription	Gastric	stomach
35	chr3:111587200-111597200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
37	chr3:111587600-111590000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:111587600-111590200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:111587800-111589800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:111587800-111591200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:111587800-111599200	Weak transcription	Liver	Liver
42	chr3:111588000-111589800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:111588000-111593800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:111588200-111589800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:111588400-111589800	Enhancers	NHDF-Ad	bronchial
46	chr3:111588400-111590000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:111588400-111590000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:111588600-111590200	Enhancers	Fetal Lung	lung
49	chr3:111588600-111591000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:111588800-111592400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links