Variant report

Variant	rs1459748
Chromosome Location	chr4:151158031-151158032
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	chr4:151151694..151154346-chr4:151156104..151158650,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10019650	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031796	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12507489	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13107340	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459745	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459751	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459752	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1563790	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169086	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2359927	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4025876	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4532220	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696241	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6535718	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6535719	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6535720	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6843630	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7658837	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7659254	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7667318	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7699202	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699907	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9307870	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307871	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9762327	0.91[ASN][1000 genomes]
rs9997299	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997489	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9999983	0.89[EUR][1000 genomes];0.89[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	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151138800-151169800	Weak transcription	Spleen	Spleen
2	chr4:151139600-151177400	Weak transcription	Brain Substantia Nigra	brain
3	chr4:151139600-151181000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:151140000-151175000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:151142200-151172200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:151146200-151169200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:151146400-151165600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:151146600-151165600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:151150800-151170800	Weak transcription	Pancreas	Pancrea
10	chr4:151151400-151158400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:151151800-151165600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:151152000-151160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:151152400-151176400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:151152800-151164200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:151153600-151164800	Weak transcription	Right Atrium	heart
16	chr4:151153800-151158400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:151155000-151160400	Enhancers	NHLF	lung
18	chr4:151155200-151160600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:151155200-151161600	Genic enhancers	HSMM	muscle
20	chr4:151156000-151159200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:151156200-151159200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:151156200-151160800	Weak transcription	Brain Anterior Caudate	brain
23	chr4:151156200-151173000	Weak transcription	Fetal Intestine Small	intestine
24	chr4:151156400-151158600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:151156400-151159000	Enhancers	Rectal Smooth Muscle	rectum
26	chr4:151156400-151163600	Weak transcription	Aorta	Aorta
27	chr4:151156400-151165200	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:151156400-151165600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:151156400-151169000	Weak transcription	Adipose Nuclei	Adipose
30	chr4:151156400-151169400	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:151156400-151170600	Weak transcription	Right Ventricle	heart
32	chr4:151156400-151174200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:151156600-151158600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:151156600-151158800	Enhancers	Colon Smooth Muscle	Colon
35	chr4:151156600-151159200	Enhancers	Fetal Lung	lung
36	chr4:151156800-151158200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:151156800-151158800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr4:151156800-151159000	Enhancers	Fetal Stomach	stomach
39	chr4:151156800-151159200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:151156800-151159200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:151157000-151158200	Enhancers	Ovary	ovary
42	chr4:151157000-151158400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr4:151157000-151159200	Flanking Active TSS	NH-A	brain
44	chr4:151157000-151159400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:151157000-151160400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:151157000-151167800	Weak transcription	Fetal Brain Female	brain
47	chr4:151157200-151158400	Enhancers	Stomach Smooth Muscle	stomach
48	chr4:151157200-151158800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:151157200-151160000	Enhancers	Osteobl	bone
50	chr4:151157400-151158200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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