Variant report

Variant	rs12714305
Chromosome Location	chr2:30590774-30590775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30585635..30588631-chr2:30590079..30592633,2	K562	blood:
2	chr2:30581763..30583811-chr2:30589547..30591280,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11885422	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022414	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33998876	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34113782	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707509	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6733641	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73925153	0.90[EUR][1000 genomes]
rs7578449	0.85[MEX][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs7603554	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7608507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv873769	chr2:30585638-30625264	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12714305	PREB	cis	parietal	SCAN
rs12714305	EHD3	cis	lymphoblastoid	seeQTL
rs12714305	FAM179A	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30582000-30591600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:30583200-30591400	Weak transcription	Gastric	stomach
3	chr2:30585400-30591200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:30585600-30605800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:30586200-30591000	Weak transcription	Fetal Kidney	kidney
6	chr2:30586200-30594800	Weak transcription	Ovary	ovary
7	chr2:30586400-30591000	Weak transcription	HSMM	muscle
8	chr2:30586400-30591400	Weak transcription	Aorta	Aorta
9	chr2:30586600-30591000	Weak transcription	HSMMtube	muscle
10	chr2:30586600-30594600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:30587000-30591000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:30587400-30593000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:30587600-30591600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:30588400-30597800	Enhancers	NHDF-Ad	bronchial
15	chr2:30588800-30591600	Enhancers	NH-A	brain
16	chr2:30589000-30591600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:30589000-30592200	Enhancers	NHLF	lung
18	chr2:30589200-30591000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:30589200-30592000	Weak transcription	Thymus	Thymus
20	chr2:30589600-30590800	Weak transcription	Fetal Heart	heart
21	chr2:30589600-30591000	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:30589600-30593800	Weak transcription	Primary B cells from cord blood	blood
23	chr2:30589600-30594800	Weak transcription	Placenta	Placenta
24	chr2:30589800-30591000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:30589800-30591000	Weak transcription	Right Atrium	heart
26	chr2:30589800-30591000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:30589800-30591200	Weak transcription	Esophagus	oesophagus
28	chr2:30589800-30591200	Weak transcription	Spleen	Spleen
29	chr2:30589800-30593600	Weak transcription	Fetal Thymus	thymus
30	chr2:30589800-30594800	Weak transcription	Adipose Nuclei	Adipose
31	chr2:30589800-30594800	Weak transcription	Left Ventricle	heart
32	chr2:30589800-30595800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:30590000-30593800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:30590400-30590800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:30590400-30591000	Enhancers	Osteobl	bone
36	chr2:30590400-30592400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:30590400-30594000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:30590600-30591600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:30590600-30591800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:30590600-30591800	Enhancers	Fetal Lung	lung
41	chr2:30590600-30592200	Enhancers	Pancreas	Pancrea
42	chr2:30590600-30592800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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