Variant report

Variant	rs256997
Chromosome Location	chr5:114918842-114918843
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	chr5:114912124..114914519-chr5:114916578..114919420,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10055677	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12187973	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13164545	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs13186296	0.89[EUR][1000 genomes]
rs171774	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173965	0.94[ASN][1000 genomes]
rs173966	0.95[ASN][1000 genomes]
rs2169771	0.81[ASN][1000 genomes]
rs2303747	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2546486	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2546487	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2559990	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs256942	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256943	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs256944	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256947	0.90[EUR][1000 genomes]
rs256948	0.91[EUR][1000 genomes]
rs256949	0.90[EUR][1000 genomes]
rs256950	0.90[EUR][1000 genomes]
rs256951	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs256952	0.90[EUR][1000 genomes]
rs256953	0.90[EUR][1000 genomes]
rs256954	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs256955	0.84[CEU][hapmap]
rs256956	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs256959	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs256964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256967	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256968	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs256969	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256970	0.94[ASN][1000 genomes]
rs256971	0.93[ASN][1000 genomes]
rs256972	0.93[ASN][1000 genomes]
rs256976	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs256978	0.90[ASN][1000 genomes]
rs256980	0.82[ASN][1000 genomes]
rs256984	0.93[ASN][1000 genomes]
rs256986	0.92[ASN][1000 genomes]
rs256987	0.96[ASN][1000 genomes]
rs256988	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256991	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256993	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256994	0.87[ASN][1000 genomes]
rs256996	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs256998	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377290	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3822579	0.89[EUR][1000 genomes]
rs387718	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs400570	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs413059	0.89[EUR][1000 genomes]
rs415577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4920967	0.88[EUR][1000 genomes]
rs698365	0.96[CEU][hapmap]
rs698366	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs698367	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7702283	0.90[EUR][1000 genomes]
rs7702869	0.90[EUR][1000 genomes]
rs7702881	0.90[EUR][1000 genomes]
rs790825	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs813761	0.86[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114901400-114922400	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:114909000-114919200	Weak transcription	Left Ventricle	heart
3	chr5:114909000-114919200	Weak transcription	Psoas Muscle	Psoas
4	chr5:114910400-114925200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:114910400-114929400	Weak transcription	Adipose Nuclei	Adipose
6	chr5:114911200-114935600	Weak transcription	Gastric	stomach
7	chr5:114911800-114922400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:114912000-114924600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:114912200-114919200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:114912200-114919200	Weak transcription	HMEC	breast
11	chr5:114912200-114920400	Weak transcription	NHEK	skin
12	chr5:114912200-114921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:114912600-114919200	Weak transcription	HUVEC	blood vessel
14	chr5:114913000-114935200	Weak transcription	Aorta	Aorta
15	chr5:114913600-114924400	Weak transcription	Placenta	Placenta
16	chr5:114913800-114919200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:114913800-114921000	Weak transcription	Fetal Lung	lung
18	chr5:114914400-114936200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:114914800-114937400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:114915200-114924600	Weak transcription	Primary B cells from cord blood	blood
21	chr5:114915400-114921400	Weak transcription	Brain Anterior Caudate	brain
22	chr5:114915600-114919200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:114915600-114919400	Weak transcription	Hela-S3	cervix
24	chr5:114915600-114921200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:114915600-114924000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:114916400-114919200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr5:114916400-114920400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:114916400-114921400	Weak transcription	Lung	lung
29	chr5:114916800-114919200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:114917000-114919200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:114917000-114921200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr5:114917400-114919000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr5:114918400-114920400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:114918600-114919400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:114918600-114919400	Enhancers	HSMM	muscle
36	chr5:114918600-114919600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr5:114918600-114919800	Enhancers	GM12878-XiMat	blood
38	chr5:114918600-114919800	Enhancers	HSMMtube	muscle
39	chr5:114918600-114920400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:114918600-114920600	Enhancers	Osteobl	bone
41	chr5:114918600-114922800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:114918600-114922800	Enhancers	NHDF-Ad	bronchial
43	chr5:114918800-114919000	Enhancers	NHLF	lung
44	chr5:114918800-114919600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:114918800-114919800	Enhancers	NH-A	brain
46	chr5:114918800-114920000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:114918800-114920000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr5:114918800-114920200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links