Variant report

Variant	rs28689052
Chromosome Location	chr16:70379770-70379771
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:70379633-70380295	GM12891	blood:	n/a	n/a
2	POLR2A	chr16:70379404-70380250	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:70379511-70380262	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr16:70379256-70381292	K562	blood:	n/a	n/a
5	POLR2A	chr16:70379669-70380090	HL-60	blood:	n/a	n/a
6	POLR2A	chr16:70379767-70381415	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr16:70379634-70380179	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:70378654-70381718	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:70379543-70381130	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr16:70379218-70380236	GM12892	blood:	n/a	n/a
11	POLR2A	chr16:70379543-70381494	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr16:70379698-70380194	HCT-116	colon:	n/a	n/a
13	POLR2A	chr16:70379665-70380288	GM12892	blood:	n/a	n/a
14	POLR2A	chr16:70379689-70380094	K562	blood:	n/a	n/a
15	POLR2A	chr16:70379386-70381232	MCF-7	breast:	n/a	n/a
16	POLR2A	chr16:70379750-70380307	GM12892	blood:	n/a	n/a
17	POLR2A	chr16:70379578-70380237	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr16:70379586-70380300	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr16:70379352-70380075	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr16:70379629-70380247	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr16:70379710-70380193	HepG2	liver:	n/a	n/a
22	POLR2A	chr16:70378915-70380288	GM12878	blood:	n/a	n/a
23	HEY1	chr16:70379657-70380167	K562	blood:	n/a	n/a
24	POLR2A	chr16:70379060-70381394	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr16:70379568-70379845	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr16:70379696-70380066	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70379447..70384942-chr16:70556059..70561583,7	K562	blood:
2	chr16:70321381..70324414-chr16:70379252..70382918,7	MCF-7	breast:
3	chr16:70379064..70380688-chr16:70557670..70559331,2	MCF-7	breast:
4	chr16:70379206..70382816-chr16:70556059..70558953,4	K562	blood:
5	chr16:70379526..70383319-chr16:70470652..70474068,4	K562	blood:
6	chr16:70379511..70381084-chr16:70487337..70489597,2	MCF-7	breast:
7	chr16:70379157..70381349-chr16:70561785..70563465,2	MCF-7	breast:
8	chr16:70318554..70325188-chr16:70378714..70382302,15	K562	blood:
9	chr16:70332853..70335232-chr16:70378695..70381623,2	K562	blood:
10	chr16:70321709..70323528-chr16:70379604..70382270,2	MCF-7	breast:
11	chr16:70378223..70384231-chr16:70413255..70416872,7	MCF-7	breast:
12	chr16:70320111..70324850-chr16:70378173..70382680,12	K562	blood:
13	chr14:69261001..69262599-chr16:70379139..70381962,2	MCF-7	breast:

No data

Variant related genes	Relation type
DDX19A	TF binding region
ENSG00000090861	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000157350	Chromatin interaction
ENSG00000260537	Chromatin interaction
ENSG00000103051	Chromatin interaction
ENSG00000221514	Chromatin interaction
ENSG00000157349	Chromatin interaction
ENSG00000260111	Chromatin interaction
ENSG00000157353	Chromatin interaction
ENSG00000189091	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13330203	1.00[AMR][1000 genomes]
rs13335135	1.00[EUR][1000 genomes]
rs17883840	1.00[EUR][1000 genomes]
rs28605415	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28827617	1.00[AMR][1000 genomes]
rs28848878	1.00[AMR][1000 genomes]
rs3972068	1.00[AMR][1000 genomes]
rs7189290	1.00[AMR][1000 genomes]
rs7191466	1.00[EUR][1000 genomes]
rs7195180	1.00[AMR][1000 genomes]
rs7200890	1.00[AMR][1000 genomes]
rs7202183	1.00[EUR][1000 genomes]
rs7202561	1.00[EUR][1000 genomes]
rs8056474	1.00[EUR][1000 genomes]
rs9931559	1.00[AMR][1000 genomes]
rs9936419	1.00[EUR][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	nsv482577	chr16:70329048-70516069	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	esv3390669	chr16:70363244-70400179	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70334200-70379800	Weak transcription	Stomach Mucosa	stomach
2	chr16:70349600-70379800	Weak transcription	Fetal Brain Male	brain
3	chr16:70357200-70380200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:70368200-70380200	Weak transcription	Small Intestine	intestine
5	chr16:70368400-70379800	Weak transcription	Hela-S3	cervix
6	chr16:70368800-70379800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr16:70368800-70379800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr16:70368800-70379800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr16:70369000-70379800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:70369000-70379800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr16:70369000-70379800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr16:70369000-70379800	Weak transcription	Aorta	Aorta
13	chr16:70369000-70379800	Weak transcription	Colon Smooth Muscle	Colon
14	chr16:70369000-70379800	Weak transcription	Esophagus	oesophagus
15	chr16:70369000-70379800	Weak transcription	Fetal Kidney	kidney
16	chr16:70369000-70379800	Weak transcription	Fetal Lung	lung
17	chr16:70369000-70379800	Weak transcription	Gastric	stomach
18	chr16:70369000-70379800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr16:70369000-70379800	Weak transcription	HSMMtube	muscle
20	chr16:70369000-70379800	Weak transcription	NH-A	brain
21	chr16:70369000-70379800	Weak transcription	NHDF-Ad	bronchial
22	chr16:70369200-70379800	Weak transcription	Primary T cells from cord blood	blood
23	chr16:70369200-70379800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr16:70369200-70379800	Weak transcription	Brain Substantia Nigra	brain
25	chr16:70369400-70379800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr16:70369400-70379800	Weak transcription	Brain Angular Gyrus	brain
27	chr16:70369400-70379800	Weak transcription	Brain Anterior Caudate	brain
28	chr16:70369400-70379800	Weak transcription	Colonic Mucosa	Colon
29	chr16:70369400-70379800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr16:70369400-70379800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr16:70369400-70379800	Weak transcription	NHLF	lung
32	chr16:70369400-70380000	Weak transcription	Ovary	ovary
33	chr16:70369400-70380200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr16:70369600-70379800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr16:70369600-70379800	Weak transcription	Right Ventricle	heart
36	chr16:70369800-70379800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr16:70370000-70379800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr16:70370600-70379800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr16:70370600-70379800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr16:70370600-70379800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr16:70370600-70379800	Weak transcription	HSMM	muscle
42	chr16:70370600-70380600	Weak transcription	Spleen	Spleen
43	chr16:70371000-70379800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:70371000-70379800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr16:70371000-70379800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:70371000-70379800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr16:70371000-70379800	Weak transcription	Thymus	Thymus
48	chr16:70371000-70380200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr16:70372200-70379800	Weak transcription	Osteobl	bone
50	chr16:70373000-70379800	Weak transcription	Fetal Intestine Small	intestine

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