Variant report

Variant	rs4889563
Chromosome Location	chr16:31880599-31880600
allele	A/T
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	RUNX3	chr16:31879976-31880613	GM12878	blood:	n/a	n/a
2	ARID3A	chr16:31880586-31880614	K562	blood:	n/a	n/a
3	RAD21	chr16:31879703-31880607	SK-N-SH	brain:	n/a	chr16:31880096-31880115 chr16:31880100-31880110 chr16:31880099-31880112 chr16:31880105-31880114 chr16:31880100-31880114
4	CTCF	chr16:31879454-31880772	SK-N-SH	brain:	n/a	chr16:31880099-31880115 chr16:31880093-31880114 chr16:31880100-31880113 chr16:31880098-31880116 chr16:31880100-31880113 chr16:31880104-31880113 chr16:31880101-31880111
5	CTCF	chr16:31880560-31880710	AoAF	blood vessel:	n/a	n/a
6	CTCF	chr16:31880560-31880710	HVMF	connective:	n/a	n/a
7	STAT3	chr16:31880023-31880629	GM12878	blood:	n/a	chr16:31880592-31880599

No.	Distal block	Cell Line	Cell type
1	chr16:31723093..31725658-chr16:31880416..31882671,2	MCF-7	breast:
2	chr16:31469205..31472299-chr16:31879583..31882157,3	MCF-7	breast:
3	chr16:31880244..31883180-chr16:31883770..31886607,4	K562	blood:
4	chr16:31710665..31714360-chr16:31877425..31881145,4	MCF-7	breast:
5	chr16:31878665..31883270-chr16:31884134..31887533,7	K562	blood:
6	chr16:31198405..31200147-chr16:31878787..31881562,2	K562	blood:
7	chr16:31461549..31464190-chr16:31877877..31881538,3	MCF-7	breast:

Variant related genes	Relation type
ZNF267	TF binding region
ENSG00000131797	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000197302	Chromatin interaction
ENSG00000260568	Chromatin interaction
ENSG00000185947	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000261731	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10871460	0.90[EUR][1000 genomes]
rs11150650	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11150651	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12444740	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12599066	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12919368	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12924931	0.96[EUR][1000 genomes]
rs1506907	1.00[CEU][hapmap]
rs1827959	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1828131	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1857943	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2358778	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3843960	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3843961	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3850114	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3861268	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3861270	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3913868	0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3913870	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3913871	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4026652	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4026653	0.92[AFR][1000 genomes]
rs4026654	1.00[CEU][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4402587	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889517	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4889518	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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889567	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889568	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889569	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6565290	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6565291	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7197804	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7200162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7202831	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7203345	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7205034	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8048908	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs8056158	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs8058598	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8059500	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8060276	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8062514	1.00[CEU][hapmap]
rs9788838	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9921760	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9928574	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9928704	1.00[CEU][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	esv3446880	chr16:31734687-31891223	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	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
8	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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31879800-31882200	Enhancers	Primary B cells from peripheral blood	blood
2	chr16:31880000-31880600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr16:31880000-31880600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr16:31880000-31880600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr16:31880000-31880600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr16:31880000-31880600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr16:31880000-31880600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr16:31880000-31880600	Flanking Active TSS	Dnd41	blood
9	chr16:31880000-31880800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr16:31880000-31880800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr16:31880000-31881200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr16:31880000-31881400	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr16:31880000-31881400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr16:31880000-31881400	Enhancers	HSMM	muscle
15	chr16:31880000-31881400	Enhancers	NHEK	skin
16	chr16:31880000-31881600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr16:31880000-31881600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:31880000-31881800	Enhancers	Fetal Thymus	thymus
19	chr16:31880000-31882000	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr16:31880000-31882000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr16:31880000-31882400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr16:31880200-31880600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr16:31880200-31880600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr16:31880200-31880600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr16:31880200-31880600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr16:31880200-31880600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr16:31880200-31880600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr16:31880200-31880600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:31880200-31880600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr16:31880200-31880600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr16:31880200-31880600	Enhancers	Brain Angular Gyrus	brain
32	chr16:31880200-31880600	Enhancers	Brain Hippocampus Middle	brain
33	chr16:31880200-31880600	Enhancers	Brain Substantia Nigra	brain
34	chr16:31880200-31880600	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr16:31880200-31880600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr16:31880200-31880600	Enhancers	Fetal Heart	heart
37	chr16:31880200-31880600	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr16:31880200-31880600	Flanking Active TSS	HUVEC	blood vessel
39	chr16:31880200-31880600	Enhancers	K562	blood
40	chr16:31880200-31880600	Flanking Active TSS	Osteobl	bone
41	chr16:31880200-31880800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr16:31880200-31880800	Enhancers	Lung	lung
43	chr16:31880200-31880800	Flanking Active TSS	Thymus	Thymus
44	chr16:31880200-31881000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:31880200-31881200	Enhancers	Hela-S3	cervix
46	chr16:31880200-31881400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr16:31880200-31881400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:31880200-31881400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr16:31880200-31881400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr16:31880200-31881400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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