Variant report

Variant	rs4889518
Chromosome Location	chr16:31907797-31907798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31907694-31907997	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:31907355-31908104	GM12892	blood:	n/a	n/a
3	POLR2A	chr16:31907317-31907851	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000259950	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10871460	0.86[EUR][1000 genomes]
rs11150650	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11150651	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12444740	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12599066	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12919368	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12924931	0.93[EUR][1000 genomes]
rs1506907	1.00[CEU][hapmap]
rs1827959	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1828131	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1857943	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2358778	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3843960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3843961	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850114	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3861268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3861270	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913868	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913870	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3913871	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4026652	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4026653	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4026654	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4402587	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889563	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889565	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]
rs4889567	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889568	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889569	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6565290	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6565291	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7185691	0.87[AFR][1000 genomes]
rs7197804	1.00[GIH][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7200162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7202831	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203345	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7205034	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8048908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8056158	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8058598	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8059500	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8060276	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8062514	1.00[CEU][hapmap]
rs9788838	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9921760	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9924259	0.82[ASW][hapmap];0.94[MKK][hapmap]
rs9928574	0.96[EUR][1000 genomes]
rs9928704	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31889400-31911600	ZNF genes & repeats	Primary B cells from cord blood	blood
2	chr16:31892000-31910400	ZNF genes & repeats	GM12878-XiMat	blood
3	chr16:31893000-31913200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:31893200-31911800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr16:31893400-31911400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:31893400-31911800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:31893400-31912000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr16:31893600-31917800	Weak transcription	Colon Smooth Muscle	Colon
9	chr16:31895000-31908400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr16:31895000-31909600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
11	chr16:31895800-31910200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr16:31896600-31910400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr16:31897600-31912000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr16:31899600-31910200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr16:31900000-31908200	Strong transcription	Fetal Thymus	thymus
16	chr16:31900000-31911000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr16:31900000-31911400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:31900400-31908800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr16:31900600-31908400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr16:31900800-31907800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr16:31900800-31907800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr16:31900800-31908800	Strong transcription	Placenta	Placenta
23	chr16:31901000-31908600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr16:31901000-31908800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr16:31901200-31907800	Strong transcription	Adipose Nuclei	Adipose
26	chr16:31901800-31908000	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr16:31902000-31908000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr16:31902200-31908000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr16:31902200-31908600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr16:31902400-31907800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr16:31903000-31907800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr16:31903000-31907800	Strong transcription	Gastric	stomach
33	chr16:31903200-31908000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr16:31903400-31907800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:31903400-31908000	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr16:31903400-31908600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr16:31903400-31909800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr16:31903600-31911600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr16:31903600-31916800	Weak transcription	Stomach Mucosa	stomach
40	chr16:31904200-31908200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr16:31904800-31907800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr16:31904800-31908200	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr16:31904800-31908600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr16:31904800-31909600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr16:31904800-31909600	ZNF genes & repeats	K562	blood
46	chr16:31904800-31910200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
47	chr16:31904800-31910400	Strong transcription	HSMM	muscle
48	chr16:31905000-31907800	Strong transcription	HSMMtube	muscle
49	chr16:31905000-31908000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
50	chr16:31905000-31908000	ZNF genes & repeats	NHEK	skin

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