Variant report

Variant	rs9924829
Chromosome Location	chr16:71749799-71749800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71748955..71755873-chr16:71756069..71760101,14	MCF-7	breast:
2	chr16:71739862..71741531-chr16:71749536..71751802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000040199	Chromatin interaction
ENSG00000261513	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11075896	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11075897	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13331951	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333988	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334566	1.00[AFR][1000 genomes]
rs13337162	0.88[AFR][1000 genomes]
rs13337224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338265	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339574	0.83[AFR][1000 genomes]
rs28436203	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28487278	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556848	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28649987	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28681277	0.85[AFR][1000 genomes]
rs28712876	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28757746	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34113755	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55829421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55930830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57187537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57827931	0.83[AFR][1000 genomes]
rs58324033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60173154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7186536	0.81[AFR][1000 genomes]
rs7196013	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578257	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73580232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582231	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582271	0.83[AFR][1000 genomes]
rs73582274	0.83[AFR][1000 genomes]
rs73582278	0.83[AFR][1000 genomes]
rs73582282	0.83[AFR][1000 genomes]
rs8048170	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059131	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062948	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8063658	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9302628	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921552	0.88[AFR][1000 genomes]
rs9924862	0.88[AFR][1000 genomes]
rs9925371	0.85[AFR][1000 genomes]
rs9925712	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926077	0.85[AFR][1000 genomes]
rs9927004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928788	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930271	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930573	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930588	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933587	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933862	0.81[AFR][1000 genomes]
rs9934778	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935867	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71683800-71756600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:71693000-71756400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr16:71702000-71756200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr16:71705000-71756200	Weak transcription	Colon Smooth Muscle	Colon
5	chr16:71705000-71756800	Weak transcription	Gastric	stomach
6	chr16:71707400-71750200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:71710600-71756200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:71710600-71756400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:71710600-71756800	Weak transcription	Lung	lung
10	chr16:71711200-71756400	Weak transcription	K562	blood
11	chr16:71715800-71756000	Weak transcription	Brain Hippocampus Middle	brain
12	chr16:71716800-71756600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr16:71724400-71756000	Weak transcription	Dnd41	blood
14	chr16:71724400-71756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr16:71724600-71756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:71724800-71756000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr16:71725000-71756000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr16:71725000-71756600	Weak transcription	Left Ventricle	heart
19	chr16:71733400-71756600	Weak transcription	Aorta	Aorta
20	chr16:71733800-71756000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr16:71734000-71756400	Weak transcription	Liver	Liver
22	chr16:71734000-71756600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr16:71734000-71756600	Weak transcription	Thymus	Thymus
24	chr16:71734000-71756800	Weak transcription	Pancreas	Pancrea
25	chr16:71734200-71756200	Weak transcription	Fetal Lung	lung
26	chr16:71735000-71755800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr16:71736000-71756400	Weak transcription	Brain Substantia Nigra	brain
28	chr16:71736400-71753200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr16:71736600-71756000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr16:71741600-71756800	Weak transcription	Small Intestine	intestine
31	chr16:71741800-71756600	Weak transcription	Psoas Muscle	Psoas
32	chr16:71742000-71755800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr16:71742000-71756000	Weak transcription	Primary B cells from cord blood	blood
34	chr16:71742000-71756000	Weak transcription	Fetal Brain Female	brain
35	chr16:71742000-71756000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr16:71742000-71756200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr16:71742000-71756400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr16:71742000-71756600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr16:71742000-71756800	Weak transcription	Spleen	Spleen
40	chr16:71742400-71756000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:71742400-71756000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr16:71743600-71756400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr16:71743800-71756200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr16:71743800-71756200	Weak transcription	NH-A	brain
45	chr16:71744000-71756000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr16:71744000-71756000	Weak transcription	Ovary	ovary
47	chr16:71744200-71752200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:71744200-71755400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr16:71744200-71756000	Weak transcription	Colonic Mucosa	Colon
50	chr16:71744200-71756000	Weak transcription	NHEK	skin

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