Variant report

Variant	rs1026740
Chromosome Location	chr4:762963-762964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr4:762854-763032	K562	blood:	n/a	n/a
2	POLR2A	chr4:762698-763195	K562	blood:	n/a	n/a
3	POLR2A	chr4:762734-763714	MCF-7	breast:	n/a	n/a
4	POLR2A	chr4:762919-763022	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr4:762812-763092	HCT-116	colon:	n/a	n/a
6	POLR2A	chr4:762763-763144	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr4:762735-763692	GM12892	blood:	n/a	n/a
8	POLR2A	chr4:762943-763146	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:762835-763017	A549	lung:	n/a	n/a
10	POLR2A	chr4:755285-762979	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr4:762616-763726	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr4:762777-763744	HepG2	liver:	n/a	n/a
13	POLR2A	chr4:762803-763147	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:762626-764386	GM12892	blood:	n/a	n/a
15	POLR2A	chr4:762805-763218	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr4:762642-763737	K562	blood:	n/a	n/a
17	POLR2A	chr4:753739-764687	K562	blood:	n/a	n/a
18	POLR2A	chr4:762899-763254	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr4:762823-763132	A549	lung:	n/a	n/a
20	POLR2A	chr4:762731-764461	GM12891	blood:	n/a	n/a
21	ZMIZ1	chr4:762835-763035	K562	blood:	n/a	n/a
22	POLR2A	chr4:762884-763287	GM12892	blood:	n/a	n/a
23	POLR2A	chr4:762823-763024	A549	lung:	n/a	n/a
24	POLR2A	chr4:762705-762988	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr4:762805-764419	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:762743-763174	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr4:762724-763084	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr4:762794-763136	K562	blood:	n/a	n/a
29	POLR2A	chr4:762725-763243	GM12891	blood:	n/a	n/a
30	POLR2A	chr4:762717-763783	GM12878	blood:	n/a	n/a
31	POLR2A	chr4:762874-763359	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr4:762808-763143	K562	blood:	n/a	n/a
33	POLR2A	chr4:762723-764268	GM12891	blood:	n/a	n/a
34	POLR2A	chr4:762764-764432	HepG2	liver:	n/a	n/a
35	POLR2A	chr4:762811-763105	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr4:762762-764399	GM12892	blood:	n/a	n/a
37	POLR2A	chr4:762639-763714	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr4:762910-763728	GM12891	blood:	n/a	n/a
39	POLR2A	chr4:762825-763020	A549	lung:	n/a	n/a
40	POLR2A	chr4:762791-763776	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr4:762732-763178	HL-60	blood:	n/a	n/a
42	POLR2A	chr4:762706-763271	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr4:762780-763118	GM12878	blood:	n/a	n/a
44	POLR2A	chr4:762743-763071	HepG2	liver:	n/a	n/a
45	JUND	chr4:762889-763000	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr4:762865-763138	HCT-116	colon:	n/a	n/a
47	POLR2A	chr4:762836-763253	H1-hESC	embryonic stem cell:	n/a	n/a
48	HMGN3	chr4:762810-763011	K562	blood:	n/a	n/a
49	BCL3	chr4:762790-763108	K562	blood:	n/a	n/a
50	POLR2A	chr4:762810-763161	HUVEC	blood vessel:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:724546..727209-chr4:762893..765350,2	K562	blood:
2	chr4:760680..763356-chr4:818980..821641,2	MCF-7	breast:
3	chr4:758084..763800-chr4:770671..778725,12	MCF-7	breast:
4	chr4:743968..746769-chr4:761390..763211,2	MCF-7	breast:
5	chr4:723040..724822-chr4:760521..763494,2	K562	blood:
6	chr4:761315..764125-chr4:766896..769678,2	MCF-7	breast:
7	chr4:761155..763075-chr4:828967..831946,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233799	TF binding region
ENSG00000260262	Chromatin interaction
ENSG00000249592	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000168993	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6823876	0.84[AMR][1000 genomes]
rs7377314	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv878253	chr4:708932-771587	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv4195	chr4:727187-768059	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
19	nsv818207	chr4:753944-821490	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
20	nsv878261	chr4:756686-1047794	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
21	nsv1007928	chr4:757263-813885	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv520136	chr4:759709-780883	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1026740	PCGF3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:727000-767600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:728600-763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:742600-763600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:742800-764000	Weak transcription	Small Intestine	intestine
5	chr4:744400-763400	Weak transcription	Right Atrium	heart
6	chr4:746000-773800	Weak transcription	Fetal Brain Male	brain
7	chr4:748200-763400	Weak transcription	Brain Substantia Nigra	brain
8	chr4:753600-769000	ZNF genes & repeats	Fetal Stomach	stomach
9	chr4:753600-773800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:753800-764200	ZNF genes & repeats	Aorta	Aorta
11	chr4:753800-764600	Strong transcription	Fetal Muscle Leg	muscle
12	chr4:753800-764800	Strong transcription	Fetal Lung	lung
13	chr4:753800-765400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:753800-766600	Strong transcription	Dnd41	blood
15	chr4:753800-768000	Strong transcription	Thymus	Thymus
16	chr4:753800-768400	Strong transcription	Primary T cells from cord blood	blood
17	chr4:753800-771600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr4:753800-773200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:753800-773200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:754000-764000	Strong transcription	Fetal Brain Female	brain
23	chr4:754000-771600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:754000-773600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:754200-765200	Strong transcription	Ovary	ovary
26	chr4:754200-765600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr4:754200-765600	Strong transcription	Gastric	stomach
28	chr4:754200-771600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:754400-764400	Strong transcription	Rectal Smooth Muscle	rectum
30	chr4:754400-765400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr4:754400-765400	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:754400-765600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:754400-765600	Strong transcription	HUVEC	blood vessel
34	chr4:754400-773400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:754600-763400	Weak transcription	Fetal Heart	heart
36	chr4:754600-765000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:754600-765200	Weak transcription	Psoas Muscle	Psoas
38	chr4:755200-764200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:755600-763400	Weak transcription	HSMMtube	muscle
40	chr4:755600-774200	Weak transcription	Hela-S3	cervix
41	chr4:756400-764800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:756600-766800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr4:757000-767000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:757200-766600	Strong transcription	HepG2	liver
45	chr4:757400-763400	Weak transcription	Primary B cells from cord blood	blood
46	chr4:757400-766000	Strong transcription	K562	blood
47	chr4:757400-767600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:757600-765800	Strong transcription	A549	lung
49	chr4:758200-769200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:758400-774200	Strong transcription	HUES48 Cell Line	embryonic stem cell

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