Variant report

Variant	rs4073690
Chromosome Location	chr4:57330960-57330961
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57330681-57331121	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:57330592-57331004	HCT-116	colon:	n/a	n/a
3	POLR2A	chr4:57330066-57331239	U87	brain:	n/a	n/a
4	POLR2A	chr4:57326457-57334588	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:57329051-57334155	U87	brain:	n/a	n/a
6	POLR2A	chr4:57328023-57334626	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr4:57330814-57331143	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:57329789-57332333	U87	brain:	n/a	n/a
9	POLR2A	chr4:57330708-57331125	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:57330793-57331067	K562	blood:	n/a	n/a
11	BCL3	chr4:57330607-57331187	A549	lung:	n/a	n/a
12	POLR2A	chr4:57328174-57331217	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:57330784-57331092	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr4:57330673-57331081	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr4:57329197-57334826	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:57329828-57331377	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:57327841-57334590	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr4:57329439-57331320	MCF-7	breast:	n/a	n/a
19	POLR2A	chr4:57330658-57331195	GM12891	blood:	n/a	n/a
20	MTA3	chr4:57330614-57331154	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:57328083-57331197	A549	lung:	n/a	n/a
22	POLR2A	chr4:57330524-57331347	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr4:57321294-57335320	K562	blood:	n/a	n/a
24	POLR2A	chr4:57327796-57331218	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:57328291-57334478	K562	blood:	n/a	n/a
26	POLR2A	chr4:57330633-57331076	HCT-116	colon:	n/a	n/a
27	POLR2A	chr4:57328090-57334773	GM12878	blood:	n/a	n/a
28	E2F4	chr4:57330941-57331124	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr4:57330680-57331121	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr4:57326028-57334384	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr4:57330640-57331022	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr4:57330698-57331045	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:57330774-57330965	ProgFib	skin:	n/a	n/a
34	POLR2A	chr4:57329895-57334760	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr4:57329138-57331157	K562	blood:	n/a	n/a
36	POLR2A	chr4:57330605-57331230	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr4:57330646-57331099	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr4:57329172-57332331	GM12891	blood:	n/a	n/a
39	POLR2A	chr4:57329661-57334500	U87	brain:	n/a	n/a
40	POLR2A	chr4:57330575-57331117	GM12892	blood:	n/a	n/a
41	POLR2A	chr4:57330789-57330997	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:57330655-57331111	GM12891	blood:	n/a	n/a
43	POLR2A	chr4:57330578-57331174	PANC-1	pancreas:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
2	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPAT-1	chr4:57327536-57333761	NONHSAT096505

No data

Variant related genes	Relation type
SRP72	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17086860	0.87[AFR][1000 genomes]
rs2001807	0.94[AFR][1000 genomes]
rs59010837	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60112184	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6818446	0.88[AFR][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
2	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
3	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
4	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:57306800-57331000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:57315000-57331800	Weak transcription	Aorta	Aorta
9	chr4:57318800-57331600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:57319200-57331600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:57322600-57331400	Weak transcription	Fetal Kidney	kidney
12	chr4:57326400-57331800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:57326400-57332000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:57326600-57332200	Weak transcription	Colonic Mucosa	Colon
15	chr4:57326800-57331800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:57327000-57331800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:57327200-57331800	Weak transcription	Gastric	stomach
18	chr4:57327400-57331600	Weak transcription	Lung	lung
19	chr4:57327400-57331800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:57327400-57332200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:57327600-57331800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:57328800-57331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:57328800-57331200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:57328800-57331400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:57328800-57331600	Weak transcription	Liver	Liver
26	chr4:57328800-57331600	Weak transcription	NH-A	brain
27	chr4:57328800-57331800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:57328800-57332000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:57328800-57332200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:57328800-57332800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:57329000-57331000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:57329000-57331400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:57329000-57331400	Weak transcription	Fetal Lung	lung
34	chr4:57329000-57331400	Weak transcription	HUVEC	blood vessel
35	chr4:57329000-57331400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr4:57329000-57331600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:57329000-57331800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr4:57329000-57331800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:57329000-57331800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:57329200-57331600	Weak transcription	Primary B cells from cord blood	blood
41	chr4:57329200-57331600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:57329400-57331000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:57329400-57331200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:57329400-57331400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:57329400-57331400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr4:57329400-57331600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:57329400-57331600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:57329400-57331600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:57329400-57331600	Weak transcription	HSMMtube	muscle
50	chr4:57329400-57331800	Weak transcription	H1 Cell Line	embryonic stem cell

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