Variant report

Variant	rs4276156
Chromosome Location	chr3:111459669-111459670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111459238..111460946-chr3:111462346..111465281,2	MCF-7	breast:
2	chr3:111457259..111459990-chr3:111577947..111581239,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12632310	0.82[CEU][hapmap]
rs13317985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13321524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs13322494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs13325336	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17423838	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs17489748	0.81[CEU][hapmap];0.86[YRI][hapmap]
rs2292516	0.82[CEU][hapmap]
rs28479130	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28534728	0.93[EUR][1000 genomes]
rs28648833	0.93[EUR][1000 genomes]
rs28675079	0.83[EUR][1000 genomes]
rs3821919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3922706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4075549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4390898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4516581	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4542994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4634085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4682313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56052712	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56215064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57902958	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58124137	0.93[EUR][1000 genomes]
rs58663746	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60867472	0.93[EUR][1000 genomes]
rs6438012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66651424	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66786213	0.93[EUR][1000 genomes]
rs66856712	0.93[EUR][1000 genomes]
rs66975684	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6762246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6762572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6778818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6782513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6787278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6789977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790355	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790977	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6795947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67970120	0.83[EUR][1000 genomes]
rs6798476	0.82[JPT][hapmap]
rs6800047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6800065	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6800922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6802960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs73220212	0.87[ASN][1000 genomes]
rs73222475	0.93[EUR][1000 genomes]
rs73222500	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7614433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9842396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9850748	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9858228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9862472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9868898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9871034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9877777	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9880633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	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
2	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
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:111454800-111460400	Enhancers	Fetal Heart	heart
4	chr3:111454800-111464400	Weak transcription	Placenta	Placenta
5	chr3:111455000-111461000	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr3:111455800-111461000	Enhancers	Rectal Smooth Muscle	rectum
7	chr3:111456200-111465600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:111457400-111460200	Weak transcription	Fetal Kidney	kidney
9	chr3:111458000-111467000	Weak transcription	Right Ventricle	heart
10	chr3:111458600-111459800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:111458600-111459800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:111458600-111460000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:111458600-111460400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:111458600-111462200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:111458600-111464400	Weak transcription	Psoas Muscle	Psoas
16	chr3:111458600-111467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:111458800-111459800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:111458800-111459800	Enhancers	Hela-S3	cervix
19	chr3:111458800-111461800	Weak transcription	Adipose Nuclei	Adipose
20	chr3:111458800-111464800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:111458800-111466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:111459000-111460000	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:111459000-111460200	Enhancers	A549	lung
24	chr3:111459000-111460400	Enhancers	HMEC	breast
25	chr3:111459000-111462200	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:111459000-111466400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:111459000-111466400	Weak transcription	NHDF-Ad	bronchial
28	chr3:111459000-111466600	Weak transcription	Stomach Mucosa	stomach
29	chr3:111459200-111460200	Weak transcription	Left Ventricle	heart
30	chr3:111459200-111460600	Enhancers	NHEK	skin
31	chr3:111459200-111462200	Weak transcription	Pancreas	Pancrea
32	chr3:111459200-111464600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:111459200-111466400	Weak transcription	Gastric	stomach
34	chr3:111459200-111466600	Weak transcription	Osteobl	bone
35	chr3:111459400-111460000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:111459400-111465600	Weak transcription	HepG2	liver
37	chr3:111459600-111460000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links