Variant report

Variant	rs1388617
Chromosome Location	chr3:151023169-151023170
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:151021027..151023183-chr3:151044316..151046639,2	MCF-7	breast:
2	chr3:151021234..151025100-chr3:151041293..151045950,7	MCF-7	breast:
3	chr3:151017110..151019943-chr3:151020802..151024030,3	MCF-7	breast:
4	chr3:151011307..151016157-chr3:151019117..151025599,7	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10513391	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935831	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935832	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935833	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935835	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11925037	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11926145	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12107539	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12485537	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12486265	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12497019	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12637988	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13079391	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16863287	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28527299	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34347156	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34708786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35144003	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35786948	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3773621	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806636	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680307	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680315	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680356	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55705054	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56087525	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62282988	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62283022	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66524723	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66927386	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784934	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785930	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796501	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6801155	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808091	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7618206	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648875	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:151021600-151024600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:151021600-151025800	Enhancers	Placenta	Placenta
4	chr3:151021600-151026600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:151021800-151023200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:151021800-151023400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr3:151021800-151023400	Enhancers	HepG2	liver
8	chr3:151021800-151024000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:151021800-151024200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:151021800-151024600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:151021800-151024800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:151022000-151024800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:151022000-151025200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:151022200-151024800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:151022400-151023200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:151022400-151023200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr3:151022400-151023200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:151022400-151023200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:151022400-151023200	Transcr. at gene 5' and 3'	NHEK	skin
20	chr3:151022400-151023400	Enhancers	Adipose Nuclei	Adipose
21	chr3:151022400-151023800	Enhancers	Stomach Mucosa	stomach
22	chr3:151022400-151024000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:151022400-151025200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:151022400-151025600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:151022400-151025800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:151022400-151026000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:151022400-151026200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:151022400-151026400	Enhancers	NHLF	lung
29	chr3:151022600-151023200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:151022600-151023200	Enhancers	Gastric	stomach
31	chr3:151022600-151023200	Enhancers	Osteobl	bone
32	chr3:151022600-151023400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:151022600-151023400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:151022600-151023400	Flanking Active TSS	A549	lung
35	chr3:151022600-151023800	Enhancers	H9 Cell Line	embryonic stem cell
36	chr3:151022600-151023800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:151022600-151023800	Enhancers	HSMMtube	muscle
38	chr3:151022600-151024200	Enhancers	HSMM	muscle
39	chr3:151022600-151024400	Flanking Active TSS	Hela-S3	cervix
40	chr3:151022600-151024800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:151022600-151025400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr3:151022600-151026400	Enhancers	NHDF-Ad	bronchial
43	chr3:151022600-151026800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:151022800-151023200	Enhancers	Fetal Thymus	thymus
45	chr3:151022800-151023200	Enhancers	Left Ventricle	heart
46	chr3:151022800-151023200	Enhancers	NH-A	brain
47	chr3:151022800-151023400	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:151022800-151023400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:151022800-151023400	Active TSS	HMEC	breast
50	chr3:151022800-151023600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links