Variant report

Variant	rs256989
Chromosome Location	chr5:114911565-114911566
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: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10038493	0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10041776	0.84[ASN][1000 genomes]
rs10043094	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10053572	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10055339	0.89[CEU][hapmap];0.82[GIH][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap]
rs10069695	0.84[EUR][1000 genomes]
rs10073505	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10075869	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10077239	0.83[EUR][1000 genomes]
rs10079000	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1015812	0.94[ASN][1000 genomes]
rs13153908	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13184723	0.94[ASN][1000 genomes]
rs13356084	0.87[ASN][1000 genomes]
rs13357862	0.87[ASN][1000 genomes]
rs2032842	0.83[CHB][hapmap]
rs2052834	0.89[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2546484	0.88[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2559990	0.85[CEU][hapmap]
rs256938	0.88[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs256943	0.85[CEU][hapmap]
rs256962	0.85[CEU][hapmap]
rs256963	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs256965	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256968	0.85[CEU][hapmap]
rs256977	0.90[ASN][1000 genomes]
rs256995	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256996	0.85[CEU][hapmap]
rs372702	0.88[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs424434	0.82[CEU][hapmap]
rs428191	0.82[CEU][hapmap]
rs6860557	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs6892071	0.85[ASN][1000 genomes]
rs6893854	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6894123	0.88[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs746566	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MKK][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs766454	0.94[ASN][1000 genomes]
rs790824	0.85[CEU][hapmap]
rs9326964	0.86[GIH][hapmap]
rs9326969	0.85[CEU][hapmap]
rs9326970	0.83[EUR][1000 genomes]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs256989	SEMA6A	cis	cerebellum	SCAN
rs256989	TICAM2	cis	cerebellum	SCAN

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	chr5:114911000-114911600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr5:114911000-114912200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:114911000-114912200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:114911000-114912200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:114911000-114912200	Enhancers	HMEC	breast
30	chr5:114911000-114912400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:114911000-114912400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:114911000-114912600	Genic enhancers	HSMM	muscle
33	chr5:114911200-114911600	Enhancers	Hela-S3	cervix
34	chr5:114911200-114911600	Enhancers	HSMMtube	muscle
35	chr5:114911200-114911800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:114911200-114912000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:114911200-114912200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:114911200-114912200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:114911200-114912200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:114911200-114912400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:114911200-114912600	Enhancers	NHLF	lung
42	chr5:114911200-114913600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr5:114911200-114935600	Weak transcription	Gastric	stomach
44	chr5:114911400-114911600	Flanking Active TSS	NH-A	brain
45	chr5:114911400-114912400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr5:114911400-114912600	Enhancers	HUVEC	blood vessel
47	chr5:114911400-114917000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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