Variant report

Variant	rs28619389
Chromosome Location	chr16:70552805-70552806
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	chr16:70552739-70552836	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:70551573..70553695-chr16:70556838..70559540,3	K562	blood:
2	chr16:70542244..70550034-chr16:70550058..70558887,15	MCF-7	breast:
3	chr16:70551842..70553695-chr16:70555040..70558338,3	K562	blood:

Variant related genes	Relation type
SF3B3	TF binding region
ENSG00000189091	Chromatin interaction
ENSG00000103051	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs13331220	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334577	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13339216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339561	1.00[AMR][1000 genomes]
rs13339593	1.00[AMR][1000 genomes]
rs13339643	1.00[AMR][1000 genomes]
rs16970226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970260	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17878662	1.00[AMR][1000 genomes]
rs17879275	1.00[AMR][1000 genomes]
rs17881316	1.00[AMR][1000 genomes]
rs17885165	1.00[AMR][1000 genomes]
rs17886111	1.00[AMR][1000 genomes]
rs28419202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28475204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28777081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55667445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55885171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55926204	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56189591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57451547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58142695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58144908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58885322	1.00[EUR][1000 genomes]
rs59158714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59460917	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60757048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61641432	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61692284	1.00[EUR][1000 genomes]
rs6499318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7184876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7185011	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7185462	1.00[EUR][1000 genomes]
rs7186436	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7188297	1.00[AMR][1000 genomes]
rs7188474	1.00[AMR][1000 genomes]
rs7188808	1.00[AMR][1000 genomes]
rs7191191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7193228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7196773	1.00[AMR][1000 genomes]
rs7199312	1.00[AMR][1000 genomes]
rs7200586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7200978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73573163	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73573175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73578815	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578819	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8047593	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8049929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8050767	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8050782	1.00[EUR][1000 genomes]
rs8051473	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8051618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8057327	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8057732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8058754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8059200	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8061243	1.00[AMR][1000 genomes]
rs8061431	1.00[AMR][1000 genomes]
rs8062414	1.00[AMR][1000 genomes]
rs8062794	1.00[AMR][1000 genomes]
rs9302615	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9921410	1.00[AMR][1000 genomes]
rs9926355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9926435	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928617	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9928808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9929182	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929354	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929882	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9932065	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933022	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9936085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9937769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9939252	0.91[AFR][1000 genomes]
rs9940353	0.94[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	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv3522631	chr16:70551447-70553838	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2439753	chr16:70552226-70553786	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70528000-70553800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr16:70528800-70556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr16:70536600-70554000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr16:70536800-70554000	Strong transcription	Fetal Stomach	stomach
7	chr16:70537200-70554000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:70537800-70553800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr16:70537800-70553800	Strong transcription	Liver	Liver
10	chr16:70539600-70553800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr16:70539800-70553000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:70539800-70553800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:70539800-70553800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:70539800-70553800	Strong transcription	Placenta	Placenta
15	chr16:70540000-70553000	Strong transcription	Thymus	Thymus
16	chr16:70540200-70553800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:70540200-70554000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr16:70540800-70553000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr16:70541000-70553000	Strong transcription	Brain Anterior Caudate	brain
20	chr16:70541000-70554000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:70541000-70554000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr16:70541000-70554000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr16:70541000-70554000	Strong transcription	Dnd41	blood
24	chr16:70541200-70556200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr16:70542400-70553000	Strong transcription	Ovary	ovary
26	chr16:70542400-70553600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr16:70543000-70556200	Weak transcription	Fetal Heart	heart
28	chr16:70543200-70553600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr16:70543400-70553000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr16:70545000-70556200	Weak transcription	Small Intestine	intestine
31	chr16:70546200-70556400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr16:70546400-70556400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr16:70546600-70553800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr16:70546600-70553800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr16:70546600-70556400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:70546800-70556400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr16:70547000-70554600	Weak transcription	HMEC	breast
38	chr16:70547800-70553400	Strong transcription	Fetal Intestine Small	intestine
39	chr16:70548400-70554400	Weak transcription	HUVEC	blood vessel
40	chr16:70548600-70553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr16:70548600-70554600	Weak transcription	NHEK	skin
42	chr16:70548800-70556000	Weak transcription	Psoas Muscle	Psoas
43	chr16:70548800-70556200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr16:70550000-70556200	Weak transcription	Fetal Brain Male	brain
45	chr16:70550200-70554400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:70550400-70556800	Weak transcription	Esophagus	oesophagus
47	chr16:70551200-70555000	Weak transcription	Right Ventricle	heart
48	chr16:70551200-70556800	Weak transcription	Aorta	Aorta
49	chr16:70551400-70553800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr16:70551400-70554800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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