Variant report

Variant	rs4889569
Chromosome Location	chr16:31920229-31920230
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10871460	0.86[EUR][1000 genomes]
rs11150650	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11150651	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12444740	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12599066	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12919368	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12924931	0.93[EUR][1000 genomes]
rs1506907	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1827959	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1828131	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1857943	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2358778	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3843960	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3843961	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850114	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3861268	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3861270	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913868	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913870	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913871	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4026652	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4026653	0.81[EUR][1000 genomes]
rs4026654	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4402587	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889517	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4889518	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889563	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889565	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889567	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889568	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6565290	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6565291	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7197804	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7200162	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7202831	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203345	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7205034	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8048908	1.00[CEU][hapmap]
rs8056158	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs8058598	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8059500	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8060276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8062514	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9788838	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9921760	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9928574	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9928704	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9929494	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv833196	chr16:31897381-32068953	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv1850460	chr16:31905688-32097085	Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31907600-31921400	Weak transcription	Hela-S3	cervix
2	chr16:31907800-31924400	Weak transcription	HSMMtube	muscle
3	chr16:31908000-31924600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:31909600-31920800	Weak transcription	K562	blood
5	chr16:31910400-31922400	Weak transcription	HSMM	muscle
6	chr16:31917000-31921000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:31917000-31921400	ZNF genes & repeats	Liver	Liver
8	chr16:31917000-31921800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr16:31917000-31921800	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr16:31917000-31921800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr16:31917000-31921800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:31917000-31922000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr16:31917000-31931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr16:31917000-31931600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr16:31917000-31932000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
16	chr16:31917000-31932200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr16:31917000-31932400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr16:31917000-31932400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr16:31917000-31934000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:31917000-31935200	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr16:31917000-31935400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:31917200-31921800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr16:31917200-31930600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr16:31917200-31930800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
25	chr16:31917200-31931600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr16:31917400-31930200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr16:31917400-31930600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:31917600-31920800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:31917600-31921400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
30	chr16:31917600-31923400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr16:31917800-31921000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
32	chr16:31918000-31930400	ZNF genes & repeats	A549	lung
33	chr16:31918200-31922600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr16:31918200-31924400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr16:31918200-31924400	Weak transcription	Pancreas	Pancrea
36	chr16:31918200-31924400	Weak transcription	Thymus	Thymus
37	chr16:31918400-31924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:31918800-31923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr16:31919400-31921400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
40	chr16:31919600-31920400	Weak transcription	Ovary	ovary
41	chr16:31919600-31930400	ZNF genes & repeats	Dnd41	blood
42	chr16:31919800-31920400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr16:31920000-31920800	ZNF genes & repeats	Placenta	Placenta
44	chr16:31920200-31921200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr16:31920200-31922800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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