Variant report

Variant	rs56823218
Chromosome Location	chr6:64283846-64283847
allele	C/T
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	CTCF	chr6:64283778-64283917	ProgFib	skin:	n/a	n/a
2	EP300	chr6:64283327-64284833	GM12878	blood:	n/a	chr6:64284626-64284635 chr6:64284625-64284634
3	CTCF	chr6:64283760-64283910	GM12871	blood:	n/a	n/a
4	MBD4	chr6:64282937-64285652	HepG2	liver:	n/a	n/a
5	MAZ	chr6:64281795-64284587	K562	blood:	n/a	chr6:64282020-64282029 chr6:64282925-64282935 chr6:64282281-64282291 chr6:64283538-64283548 chr6:64282265-64282275
6	CTCF	chr6:64283660-64283930	NHLF	lung:	n/a	n/a
7	POLR2A	chr6:64281699-64283884	A549	lung:	n/a	n/a
8	POLR2A	chr6:64282913-64284595	PFSK-1	brain:	n/a	n/a
9	TAF1	chr6:64281774-64283895	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr6:64283829-64283895	MCF-7	breast:	n/a	n/a
11	POLR2A	chr6:64281756-64284414	ProgFib	skin:	n/a	n/a
12	POLR2A	chr6:64281534-64284532	GM18526	blood:	n/a	n/a
13	RFX5	chr6:64283391-64284015	HepG2	liver:	n/a	n/a
14	HCFC1	chr6:64282978-64283945	K562	blood:	n/a	n/a
15	FOXA1	chr6:64283440-64283981	T-47D	breast:	n/a	n/a
16	SP1	chr6:64283320-64283897	A549	lung:	n/a	chr6:64283538-64283552 chr6:64283537-64283549 chr6:64283538-64283547 chr6:64283537-64283548 chr6:64283538-64283548 chr6:64283539-64283548 chr6:64283537-64283549
17	POLR2A	chr6:64281683-64283883	ECC-1	luminal epithelium:	n/a	n/a
18	NFATC1	chr6:64283044-64284498	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:64281938-64284042	HUVEC	blood vessel:	n/a	n/a
20	ELK4	chr6:64283314-64283963	Hela-S3	cervix:	n/a	n/a
21	PML	chr6:64281379-64284728	GM12878	blood:	n/a	chr6:64284627-64284636 chr6:64281829-64281838 chr6:64284624-64284633
22	HEY1	chr6:64281682-64284600	K562	blood:	n/a	chr6:64283529-64283544 chr6:64282276-64282291 chr6:64282913-64282928 chr6:64282238-64282253
23	CREB1	chr6:64281310-64284649	HepG2	liver:	n/a	n/a
24	MAX	chr6:64282984-64283964	SK-N-SH	brain:	n/a	chr6:64283538-64283548
25	CTCF	chr6:64283804-64283981	GM13977	blood:	n/a	n/a
26	CTCF	chr6:64283800-64283950	AG09319	gingival:	n/a	n/a
27	EP300	chr6:64283314-64284479	GM12878	blood:	n/a	n/a
28	CTCF	chr6:64283121-64284790	A549	lung:	n/a	chr6:64284392-64284410 chr6:64284396-64284403 chr6:64284394-64284415 chr6:64284395-64284408
29	STAT5A	chr6:64281685-64284185	GM12878	blood:	n/a	chr6:64282170-64282182 chr6:64282175-64282187
30	RAD21	chr6:64283490-64284054	SK-N-SH_RA	brain:	n/a	n/a
31	CTCF	chr6:64283734-64283885	Spleen_OC	spleen:	n/a	n/a
32	PML	chr6:64283195-64283923	K562	blood:	n/a	n/a
33	BHLHE40	chr6:64283005-64283951	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:64282798-64284638	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr6:64283700-64283850	SAEC	small airway:	n/a	n/a
36	ZNF263	chr6:64282989-64284626	HEK293-T-REx	kidney:	n/a	chr6:64283545-64283554
37	CTCF	chr6:64283800-64283950	HepG2	liver:	n/a	n/a
38	WRNIP1	chr6:64283219-64284519	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:64281673-64284840	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr6:64280071-64285528	MCF10A-Er-Src	breast:	n/a	n/a
41	POU2F2	chr6:64282789-64283936	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:64281915-64284104	K562	blood:	n/a	n/a
43	TAF1	chr6:64281965-64283871	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr6:64282808-64283932	HUVEC	blood vessel:	n/a	n/a
45	TBP	chr6:64283243-64285825	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:64282878-64284513	GM12891	blood:	n/a	n/a
47	RELA	chr6:64283040-64284568	GM12891	blood:	n/a	n/a
48	FOSL2	chr6:64282888-64283943	HepG2	liver:	n/a	n/a
49	TAF1	chr6:64283119-64283989	ECC-1	luminal epithelium:	n/a	n/a
50	CHD2	chr6:64281450-64284518	HepG2	liver:	n/a	chr6:64283784-64283791

No.	Distal block	Cell Line	Cell type
1	chr6:64028950..64031387-chr6:64282272..64283955,2	MCF-7	breast:
2	chr6:64283629..64285650-chr6:64307693..64310407,3	MCF-7	breast:
3	chr6:64228157..64231841-chr6:64281826..64284222,3	MCF-7	breast:
4	chr6:64283165..64284700-chr6:64513286..64516142,2	MCF-7	breast:
5	chr6:64282300..64285121-chr6:64344482..64347606,3	MCF-7	breast:
6	chr6:64281350..64286126-chr6:64342580..64350015,13	K562	blood:
7	chr6:64280920..64286126-chr6:64341540..64349518,16	K562	blood:
8	chr6:64062639..64063365-chr6:64283555..64284772,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266680	TF binding region
ENSG00000188107	Chromatin interaction
ENSG00000118482	Chromatin interaction
ENSG00000112245	Chromatin interaction
ENSG00000146166	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1681934	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622277	0.81[ASN][1000 genomes]
rs2627797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758240	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3373173	chr6:64281418-64284366	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
2	esv3412678	chr6:64282218-64284766	Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64280400-64285200	Active TSS	Liver	Liver
2	chr6:64281200-64284600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:64281200-64284600	Active TSS	Fetal Brain Female	brain
4	chr6:64281200-64284800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:64281400-64284000	Active TSS	Brain Substantia Nigra	brain
6	chr6:64281400-64284400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:64281400-64284600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:64281400-64284800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:64281400-64284800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:64281400-64284800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:64281400-64285000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:64281400-64285000	Active TSS	Colonic Mucosa	Colon
13	chr6:64281400-64285200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:64281400-64285400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:64281400-64285400	Active TSS	Stomach Smooth Muscle	stomach
16	chr6:64281400-64285600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:64281400-64285800	Active TSS	Fetal Intestine Large	intestine
18	chr6:64281400-64286400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr6:64281600-64284000	Active TSS	Fetal Intestine Small	intestine
20	chr6:64281600-64284200	Active TSS	Left Ventricle	heart
21	chr6:64281600-64284200	Active TSS	Pancreas	Pancrea
22	chr6:64281600-64284200	Active TSS	HSMMtube	muscle
23	chr6:64281600-64284400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:64281600-64284400	Active TSS	Fetal Muscle Trunk	muscle
25	chr6:64281600-64284600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:64281600-64284600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:64281600-64284600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:64281600-64284600	Active TSS	Placenta	Placenta
29	chr6:64281600-64284600	Active TSS	Thymus	Thymus
30	chr6:64281600-64284800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr6:64281600-64285400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:64281600-64285600	Active TSS	Psoas Muscle	Psoas
33	chr6:64281800-64284000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:64281800-64284000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:64281800-64284000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr6:64281800-64284000	Active TSS	Brain Hippocampus Middle	brain
37	chr6:64281800-64284000	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr6:64281800-64284000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr6:64281800-64284000	Active TSS	Small Intestine	intestine
40	chr6:64281800-64284200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:64281800-64284200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:64281800-64284200	Active TSS	Gastric	stomach
43	chr6:64281800-64284400	Active TSS	Aorta	Aorta
44	chr6:64281800-64284400	Active TSS	Ovary	ovary
45	chr6:64281800-64284600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr6:64281800-64285000	Active TSS	Stomach Mucosa	stomach
47	chr6:64281800-64285000	Active TSS	HMEC	breast
48	chr6:64281800-64285600	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr6:64282000-64284000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:64282000-64284000	Active TSS	Brain Angular Gyrus	brain

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