Variant report

Variant	rs28649987
Chromosome Location	chr16:71696988-71696989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71694547..71697173-chr16:71755401..71757599,2	MCF-7	breast:
2	chr16:71696881..71698945-chr16:71757287..71759170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261513	Chromatin interaction
ENSG00000040199	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11075896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11075897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13331951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333988	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334187	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334255	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334566	0.91[AFR][1000 genomes]
rs13337162	0.96[AFR][1000 genomes]
rs13337224	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339574	0.92[AFR][1000 genomes]
rs28436203	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28487278	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28681277	0.93[AFR][1000 genomes]
rs28712876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28744680	0.83[AFR][1000 genomes]
rs28757746	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34113755	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55829421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55930830	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56209933	0.83[AFR][1000 genomes]
rs57187537	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57827931	0.92[AFR][1000 genomes]
rs58324033	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60173154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61258964	0.82[AFR][1000 genomes]
rs7196013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198645	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73580232	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8048170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059131	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062948	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8063658	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9302626	0.83[AFR][1000 genomes]
rs9302628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921552	0.96[AFR][1000 genomes]
rs9924829	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9924862	0.96[AFR][1000 genomes]
rs9925371	0.93[AFR][1000 genomes]
rs9925712	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926077	0.93[AFR][1000 genomes]
rs9927004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928298	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930271	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930588	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933587	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935867	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71668000-71703000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr16:71671800-71704000	Weak transcription	Fetal Brain Male	brain
3	chr16:71672000-71741400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:71674800-71704600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr16:71675000-71724000	Weak transcription	Esophagus	oesophagus
6	chr16:71681200-71710800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:71681200-71716000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr16:71682800-71698000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr16:71683800-71704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr16:71683800-71756600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:71684000-71697800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr16:71684000-71704000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr16:71685200-71741200	Weak transcription	Psoas Muscle	Psoas
14	chr16:71685400-71718800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr16:71685800-71726000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr16:71686200-71705400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr16:71686800-71703000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr16:71686800-71717200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr16:71687000-71700200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr16:71687800-71725000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr16:71688600-71703400	Weak transcription	Pancreas	Pancrea
22	chr16:71688600-71704000	Weak transcription	Gastric	stomach
23	chr16:71689000-71703200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr16:71689000-71710000	Weak transcription	Thymus	Thymus
25	chr16:71690600-71697200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:71690600-71699400	Weak transcription	Brain Substantia Nigra	brain
27	chr16:71690600-71700200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr16:71690600-71701000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr16:71690600-71702800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr16:71690600-71703200	Weak transcription	Lung	lung
31	chr16:71690600-71703400	Weak transcription	Right Ventricle	heart
32	chr16:71690600-71706400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr16:71690600-71708800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr16:71690600-71709600	Weak transcription	Small Intestine	intestine
35	chr16:71690600-71733600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr16:71690600-71741200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr16:71690800-71699400	Weak transcription	Brain Hippocampus Middle	brain
38	chr16:71690800-71725600	Weak transcription	Fetal Thymus	thymus
39	chr16:71691200-71703800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr16:71692600-71699400	Weak transcription	A549	lung
41	chr16:71692800-71697400	Weak transcription	Fetal Brain Female	brain
42	chr16:71692800-71697600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr16:71692800-71697600	Weak transcription	HMEC	breast
44	chr16:71692800-71697600	Weak transcription	NHDF-Ad	bronchial
45	chr16:71692800-71700000	Weak transcription	Colon Smooth Muscle	Colon
46	chr16:71692800-71701200	Weak transcription	Hela-S3	cervix
47	chr16:71692800-71703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr16:71693000-71697400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr16:71693000-71697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr16:71693000-71697400	Weak transcription	NH-A	brain

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