Variant report

Variant	rs28628240
Chromosome Location	chr16:69742378-69742379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:69740530-69743833	MCF-7	breast:	n/a	n/a
2	POLR2A	chr16:69741274-69743842	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:69741755-69742876	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:69741607-69742838	K562	blood:	n/a	n/a
5	POLR2A	chr16:69741753-69742969	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr16:69742260-69742630	GM12891	blood:	n/a	n/a
7	POLR2A	chr16:69742290-69742625	A549	lung:	n/a	n/a
8	POLR2A	chr16:69742324-69742692	Hela-S3	cervix:	n/a	n/a
9	ELF1	chr16:69742369-69742725	A549	lung:	n/a	n/a
10	POLR2A	chr16:69739930-69743902	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:69742297-69743817	HCT-116	colon:	n/a	n/a
12	POLR2A	chr16:69742289-69742701	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr16:69739832-69743980	A549	lung:	n/a	n/a
14	POLR2A	chr16:69742362-69742874	U87	brain:	n/a	n/a
15	POLR2A	chr16:69742286-69742723	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:69741801-69742718	HepG2	liver:	n/a	n/a
17	JUND	chr16:69741814-69742588	A549	lung:	n/a	n/a
18	POLR2A	chr16:69742372-69742853	U87	brain:	n/a	n/a
19	POLR2A	chr16:69742271-69742876	HCT-116	colon:	n/a	n/a
20	BCL3	chr16:69740012-69743000	A549	lung:	n/a	n/a
21	POLR2A	chr16:69742313-69742604	HepG2	liver:	n/a	n/a
22	POLR2A	chr16:69742335-69742561	ProgFib	skin:	n/a	n/a
23	FOSL2	chr16:69741824-69743133	HepG2	liver:	n/a	n/a
24	POLR2A	chr16:69742266-69742447	A549	lung:	n/a	n/a
25	POLR2A	chr16:69742348-69742440	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69741680..69751385-chr16:69755023..69763559,18	MCF-7	breast:
2	chr16:69741307..69747044-chr16:69787229..69790189,11	MCF-7	breast:
3	chr16:69734561..69737941-chr16:69738671..69742586,5	MCF-7	breast:
4	chr16:69740285..69743443-chr16:69794568..69797700,3	MCF-7	breast:
5	chr16:69741703..69743553-chr16:69758543..69761964,3	MCF-7	breast:
6	chr16:69742300..69746801-chr16:69786779..69790470,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261602	TF binding region
ENSG00000198373	Chromatin interaction
ENSG00000262136	Chromatin interaction
ENSG00000141101	Chromatin interaction
ENSG00000260772	Chromatin interaction
ENSG00000181019	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs13329778	1.00[AMR][1000 genomes]
rs13329812	1.00[AMR][1000 genomes]
rs13330995	1.00[AMR][1000 genomes]
rs13332544	1.00[AMR][1000 genomes]
rs13332880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13336041	1.00[AMR][1000 genomes]
rs13336357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338911	1.00[AMR][1000 genomes]
rs13339493	1.00[AMR][1000 genomes]
rs28402794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28429826	1.00[AMR][1000 genomes]
rs28502677	1.00[AMR][1000 genomes]
rs28514573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28523536	1.00[AMR][1000 genomes]
rs28535427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28576892	1.00[AMR][1000 genomes]
rs28583989	1.00[AMR][1000 genomes]
rs28607148	1.00[AMR][1000 genomes]
rs28610117	1.00[AMR][1000 genomes]
rs28651196	1.00[AMR][1000 genomes]
rs28673794	1.00[AMR][1000 genomes]
rs28756357	1.00[AMR][1000 genomes]
rs28803823	1.00[AMR][1000 genomes]
rs28867427	1.00[AMR][1000 genomes]
rs28882509	1.00[AMR][1000 genomes]
rs7196281	1.00[AMR][1000 genomes]
rs7196801	1.00[AMR][1000 genomes]
rs74025780	1.00[AMR][1000 genomes]
rs8049348	1.00[AMR][1000 genomes]
rs9674055	1.00[AMR][1000 genomes]
rs9921301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9923096	1.00[AMR][1000 genomes]
rs9923471	1.00[AMR][1000 genomes]
rs9924073	1.00[AMR][1000 genomes]
rs9924364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9924630	1.00[AMR][1000 genomes]
rs9925245	1.00[AMR][1000 genomes]
rs9926382	1.00[AMR][1000 genomes]
rs9926822	1.00[AMR][1000 genomes]
rs9928560	1.00[AMR][1000 genomes]
rs9930692	1.00[AMR][1000 genomes]
rs9931479	1.00[AMR][1000 genomes]
rs9932104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933606	1.00[AMR][1000 genomes]
rs9933745	1.00[AMR][1000 genomes]
rs9935697	1.00[AMR][1000 genomes]
rs9935973	1.00[AMR][1000 genomes]
rs9936451	1.00[AMR][1000 genomes]
rs9937762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9938552	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	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
3	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:69726000-69755800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
4	chr16:69726800-69747600	Weak transcription	Fetal Heart	heart
5	chr16:69728200-69746200	Weak transcription	Stomach Mucosa	stomach
6	chr16:69728200-69758600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr16:69728400-69744200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:69728400-69748800	Weak transcription	Gastric	stomach
9	chr16:69728400-69759200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:69728600-69752000	Weak transcription	Fetal Brain Male	brain
11	chr16:69729200-69745000	Weak transcription	Spleen	Spleen
12	chr16:69729400-69743600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr16:69729400-69744800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr16:69729400-69745000	Weak transcription	Pancreas	Pancrea
15	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
16	chr16:69729400-69760000	Weak transcription	Ovary	ovary
17	chr16:69729600-69745000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:69729800-69746200	Weak transcription	Aorta	Aorta
19	chr16:69729800-69746200	Weak transcription	Left Ventricle	heart
20	chr16:69729800-69748800	Weak transcription	Esophagus	oesophagus
21	chr16:69730000-69743400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr16:69730000-69743400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr16:69730000-69743600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr16:69730000-69745200	Weak transcription	Thymus	Thymus
25	chr16:69730000-69745800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:69730000-69759000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr16:69730200-69742600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr16:69730200-69743400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr16:69730200-69743400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr16:69730200-69746000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:69730400-69744800	Weak transcription	Colonic Mucosa	Colon
32	chr16:69730400-69747000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:69730600-69743600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr16:69730600-69759800	Weak transcription	Fetal Brain Female	brain
35	chr16:69730800-69744600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr16:69730800-69759800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr16:69731000-69746000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr16:69731600-69743600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr16:69731800-69744400	Weak transcription	K562	blood
40	chr16:69731800-69745000	Weak transcription	Hela-S3	cervix
41	chr16:69731800-69746200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr16:69731800-69759600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr16:69731800-69759800	Weak transcription	Primary B cells from cord blood	blood
44	chr16:69731800-69759800	Weak transcription	Right Ventricle	heart
45	chr16:69732000-69743400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr16:69732000-69746200	Weak transcription	Brain Substantia Nigra	brain
47	chr16:69732600-69743400	Weak transcription	Dnd41	blood
48	chr16:69732600-69744800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:69732600-69745000	Weak transcription	Fetal Thymus	thymus
50	chr16:69733000-69744800	Weak transcription	Fetal Muscle Trunk	muscle

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