Variant report

Variant	rs4889565
Chromosome Location	chr16:31897308-31897309
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	chr16:31896123..31898130-chr16:31922083..31923795,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185947	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10871460	0.86[EUR][1000 genomes]
rs11150650	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11150651	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12444740	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12599066	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12919368	1.00[CEU][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12924931	0.93[EUR][1000 genomes]
rs1506907	1.00[CEU][hapmap]
rs1827959	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1828131	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1857943	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2358778	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3843960	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3843961	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850114	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3861268	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3861270	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913868	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913870	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913871	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4026652	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4026653	0.81[EUR][1000 genomes]
rs4026654	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4402587	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889517	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4889518	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889563	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889567	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889568	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889569	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6565290	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6565291	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7197804	1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7200162	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7202831	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203345	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7205034	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8048908	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8056158	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8058598	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8059500	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8060276	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8062514	1.00[CEU][hapmap]
rs9788838	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9921760	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9928574	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9928704	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067321	chr16:31652036-31959992	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv918074	chr16:31669781-31935033	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1063037	chr16:31669981-31934894	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv542903	chr16:31669981-31934894	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1066522	chr16:31831196-31959992	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1057300	chr16:31862900-31959992	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31886800-31897600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr16:31886800-31898200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:31886800-31901000	Weak transcription	Fetal Brain Male	brain
4	chr16:31887000-31901600	Weak transcription	Fetal Brain Female	brain
5	chr16:31887000-31902200	ZNF genes & repeats	A549	lung
6	chr16:31887200-31900800	Weak transcription	Brain Germinal Matrix	brain
7	chr16:31887400-31900800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr16:31887800-31907400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:31889400-31911600	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr16:31889600-31897600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr16:31890000-31897600	Strong transcription	Fetal Intestine Large	intestine
12	chr16:31890200-31897600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr16:31890200-31905800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr16:31891800-31901800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr16:31892000-31900800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr16:31892000-31905000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr16:31892000-31910400	ZNF genes & repeats	GM12878-XiMat	blood
18	chr16:31892200-31898800	Strong transcription	Dnd41	blood
19	chr16:31892200-31900800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr16:31892200-31901600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr16:31892200-31905000	Weak transcription	Fetal Heart	heart
22	chr16:31892400-31897400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr16:31892400-31899600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr16:31892400-31903400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr16:31892400-31904200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr16:31892400-31905000	Weak transcription	Brain Substantia Nigra	brain
27	chr16:31892400-31905800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:31892800-31898000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr16:31892800-31899000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr16:31892800-31899200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:31892800-31900800	Weak transcription	Ovary	ovary
32	chr16:31892800-31901600	Weak transcription	Brain Anterior Caudate	brain
33	chr16:31892800-31902600	Weak transcription	Pancreas	Pancrea
34	chr16:31892800-31905200	Weak transcription	Right Ventricle	heart
35	chr16:31892800-31906000	Weak transcription	Psoas Muscle	Psoas
36	chr16:31893000-31897400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:31893000-31897600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:31893000-31899400	Strong transcription	Osteobl	bone
39	chr16:31893000-31900800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr16:31893000-31913200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr16:31893200-31911800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr16:31893400-31897600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr16:31893400-31902800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr16:31893400-31911400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr16:31893400-31911800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:31893400-31912000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr16:31893600-31917800	Weak transcription	Colon Smooth Muscle	Colon
48	chr16:31893800-31903400	Strong transcription	HSMM	muscle
49	chr16:31894000-31903000	Weak transcription	Stomach Mucosa	stomach
50	chr16:31894200-31897800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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