Variant report

Variant	rs256988
Chromosome Location	chr5:114911369-114911370
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	chr5:114903873..114906375-chr5:114910655..114912171,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-11	chr5:114910746-114913269	NONHSAT103306

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10055677	0.92[EUR][1000 genomes]
rs12187973	0.85[ASN][1000 genomes]
rs13164545	0.87[EUR][1000 genomes]
rs13186296	0.90[EUR][1000 genomes]
rs171774	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs173965	0.96[ASN][1000 genomes]
rs173966	0.99[ASN][1000 genomes]
rs187682	0.83[ASN][1000 genomes]
rs2169771	0.83[ASN][1000 genomes]
rs2303747	0.87[EUR][1000 genomes]
rs2546486	0.84[ASN][1000 genomes]
rs2559990	0.85[ASN][1000 genomes]
rs256942	0.95[EUR][1000 genomes]
rs256943	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs256944	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256945	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256947	0.92[EUR][1000 genomes]
rs256948	0.92[EUR][1000 genomes]
rs256949	0.92[EUR][1000 genomes]
rs256950	0.92[EUR][1000 genomes]
rs256951	0.92[EUR][1000 genomes]
rs256952	0.92[EUR][1000 genomes]
rs256953	0.92[EUR][1000 genomes]
rs256954	0.92[EUR][1000 genomes]
rs256964	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256967	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs256968	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs256969	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256970	0.94[ASN][1000 genomes]
rs256971	0.94[ASN][1000 genomes]
rs256972	0.94[ASN][1000 genomes]
rs256978	0.90[ASN][1000 genomes]
rs256980	0.84[ASN][1000 genomes]
rs256984	0.95[ASN][1000 genomes]
rs256986	0.96[ASN][1000 genomes]
rs256987	0.99[ASN][1000 genomes]
rs256991	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256994	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs256996	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs256997	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256998	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs377290	0.95[EUR][1000 genomes]
rs3822579	0.91[EUR][1000 genomes]
rs387718	0.85[ASN][1000 genomes]
rs400570	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs413059	0.91[EUR][1000 genomes]
rs415577	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4920967	0.89[EUR][1000 genomes]
rs698366	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs698367	0.92[EUR][1000 genomes]
rs7702283	0.91[EUR][1000 genomes]
rs7702869	0.92[EUR][1000 genomes]
rs7702881	0.92[EUR][1000 genomes]
rs790825	0.95[EUR][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	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	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114901400-114922400	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:114907800-114918200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:114908200-114918600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:114908400-114912400	Enhancers	NHDF-Ad	bronchial
5	chr5:114908600-114912200	Enhancers	Osteobl	bone
6	chr5:114908800-114911600	Enhancers	GM12878-XiMat	blood
7	chr5:114908800-114915200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:114908800-114918600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:114909000-114914400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:114909000-114914400	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:114909000-114914600	Weak transcription	Brain Anterior Caudate	brain
12	chr5:114909000-114914800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:114909000-114918800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:114909000-114919200	Weak transcription	Left Ventricle	heart
15	chr5:114909000-114919200	Weak transcription	Psoas Muscle	Psoas
16	chr5:114909200-114912800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:114910200-114912200	Enhancers	NHEK	skin
18	chr5:114910200-114918400	Weak transcription	Fetal Intestine Large	intestine
19	chr5:114910400-114914400	Weak transcription	Brain Substantia Nigra	brain
20	chr5:114910400-114914600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:114910400-114925200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:114910400-114929400	Weak transcription	Adipose Nuclei	Adipose
23	chr5:114910800-114912000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:114910800-114916600	Weak transcription	Ovary	ovary
25	chr5:114911000-114911400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:114911000-114911400	Flanking Active TSS	HUVEC	blood vessel
27	chr5:114911000-114911600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr5:114911000-114912200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:114911000-114912200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:114911000-114912200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:114911000-114912200	Enhancers	HMEC	breast
32	chr5:114911000-114912400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:114911000-114912400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:114911000-114912600	Genic enhancers	HSMM	muscle
35	chr5:114911200-114911400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr5:114911200-114911400	Enhancers	NH-A	brain
37	chr5:114911200-114911600	Enhancers	Hela-S3	cervix
38	chr5:114911200-114911600	Enhancers	HSMMtube	muscle
39	chr5:114911200-114911800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:114911200-114912000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:114911200-114912200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:114911200-114912200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:114911200-114912200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:114911200-114912400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:114911200-114912600	Enhancers	NHLF	lung
46	chr5:114911200-114913600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr5:114911200-114935600	Weak transcription	Gastric	stomach

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