Variant report

Variant	rs73742544
Chromosome Location	chr6:28317536-28317537
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:267)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:267 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28317482-28317964	U87	brain:	n/a	n/a
2	NFIC	chr6:28317179-28317894	GM12878	blood:	n/a	n/a
3	NFIC	chr6:28317490-28318437	HepG2	liver:	n/a	n/a
4	POU2F2	chr6:28317536-28318199	GM12891	blood:	n/a	n/a
5	ELF1	chr6:28317530-28317960	SK-N-SH	brain:	n/a	chr6:28317684-28317693 chr6:28317683-28317694
6	NFATC1	chr6:28317434-28317945	GM12878	blood:	n/a	n/a
7	YY1	chr6:28317223-28317914	SK-N-SH_RA	brain:	n/a	n/a
8	MXI1	chr6:28317516-28318212	HepG2	liver:	n/a	n/a
9	FOXM1	chr6:28317498-28317914	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:28317494-28318244	HepG2	liver:	n/a	n/a
11	SIN3A	chr6:28317468-28318151	H1-hESC	embryonic stem cell:	n/a	chr6:28317978-28317989
12	TRIM28	chr6:28317346-28318356	K562	blood:	n/a	n/a
13	NFIC	chr6:28317495-28318455	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr6:28317530-28318081	MCF-7	breast:	n/a	n/a
15	TAF1	chr6:28317279-28318268	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr6:28317303-28318277	H1-neurons	neurons:	n/a	n/a
17	ELF1	chr6:28317265-28318265	HCT-116	colon:	n/a	chr6:28317684-28317693 chr6:28317683-28317694
18	MAFK	chr6:28317485-28317828	HepG2	liver:	n/a	n/a
19	ELF1	chr6:28317490-28318019	K562	blood:	n/a	chr6:28317684-28317693 chr6:28317683-28317694
20	REST	chr6:28317491-28317963	HepG2	liver:	n/a	n/a
21	TBL1XR1	chr6:28317264-28318493	K562	blood:	n/a	n/a
22	MAFK	chr6:28317485-28318512	K562	blood:	n/a	n/a
23	HEY1	chr6:28317497-28317952	HepG2	liver:	n/a	n/a
24	GABPA	chr6:28317340-28318157	MCF-7	breast:	n/a	n/a
25	TAF1	chr6:28317437-28318258	K562	blood:	n/a	n/a
26	YY1	chr6:28317499-28318180	GM12878	blood:	n/a	n/a
27	CHD2	chr6:28317447-28317979	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:28317315-28318037	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:28317498-28318274	K562	blood:	n/a	n/a
30	YY1	chr6:28317521-28318070	GM12892	blood:	n/a	n/a
31	KAP1	chr6:28317527-28317974	U2OS	brain:	n/a	n/a
32	POLR2A	chr6:28317498-28318188	GM19099	blood:	n/a	n/a
33	POLR2A	chr6:28317471-28318110	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:28317475-28318244	GM12892	blood:	n/a	n/a
35	POLR2A	chr6:28317380-28318350	GM12891	blood:	n/a	n/a
36	TAF1	chr6:28317457-28318025	ECC-1	luminal epithelium:	n/a	n/a
37	HEY1	chr6:28317461-28318263	K562	blood:	n/a	n/a
38	POLR2A	chr6:28317470-28318302	K562	blood:	n/a	n/a
39	GABPA	chr6:28317355-28318078	SK-N-SH	brain:	n/a	n/a
40	MYC	chr6:28317496-28317833	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr6:28317407-28318499	HL-60	blood:	n/a	n/a
42	POLR2A	chr6:28317492-28318124	GM12892	blood:	n/a	n/a
43	POLR2A	chr6:28317190-28318020	PFSK-1	brain:	n/a	n/a
44	MAX	chr6:28317432-28318259	ECC-1	luminal epithelium:	n/a	n/a
45	MAFF	chr6:28317458-28317868	HepG2	liver:	n/a	n/a
46	POLR2A	chr6:28317416-28318027	U87	brain:	n/a	n/a
47	TAF1	chr6:28317303-28318324	H1-neurons	neurons:	n/a	n/a
48	SP1	chr6:28317448-28317885	H1-hESC	embryonic stem cell:	n/a	chr6:28317703-28317712 chr6:28317619-28317628 chr6:28317702-28317713 chr6:28317618-28317630
49	ETS1	chr6:28317519-28317848	K562	blood:	n/a	chr6:28317685-28317696 chr6:28317686-28317696 chr6:28317685-28317694 chr6:28317686-28317697 chr6:28317685-28317694
50	MAX	chr6:28317476-28318031	A549	lung:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
2	chr6:28109689..28111250-chr6:28315546..28317991,2	K562	blood:
3	chr6:28103114..28106211-chr6:28315199..28319125,3	K562	blood:
4	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
5	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
6	chr6:28127970..28130555-chr6:28316475..28318965,2	K562	blood:
7	chr6:27859494..27863644-chr6:28315287..28317995,4	K562	blood:
8	chr6:27859494..27861769-chr6:28315287..28317995,2	K562	blood:
9	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
10	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
11	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:
12	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
13	chr6:28101857..28106060-chr6:28315199..28321034,6	K562	blood:
14	chr6:28315597..28319153-chr6:28366055..28369015,3	K562	blood:
15	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ZKSCAN3	TF binding region
ENSG00000197062	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10484542	0.84[AFR][1000 genomes]
rs1416919	0.84[AFR][1000 genomes]
rs16893973	0.83[AFR][1000 genomes]
rs16893975	0.83[AFR][1000 genomes]
rs17720687	0.85[ASN][1000 genomes]
rs2077474	0.90[AFR][1000 genomes]
rs2159275	0.84[AFR][1000 genomes]
rs2281040	0.84[AFR][1000 genomes]
rs2281041	0.84[AFR][1000 genomes]
rs2299030	0.83[ASN][1000 genomes]
rs58019071	0.84[AFR][1000 genomes]
rs59598126	0.84[AFR][1000 genomes]
rs60568488	0.84[AFR][1000 genomes]
rs60698636	0.93[AFR][1000 genomes]
rs723475	0.84[AFR][1000 genomes]
rs723476	0.82[AFR][1000 genomes]
rs73742535	0.84[AFR][1000 genomes]
rs73742536	0.84[AFR][1000 genomes]
rs73742539	0.84[AFR][1000 genomes]
rs73742541	0.84[AFR][1000 genomes]
rs73742545	0.93[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 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	chr6:28317000-28317600	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr6:28317000-28318000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:28317000-28318000	Active TSS	Primary hematopoietic stem cells	blood
4	chr6:28317000-28318200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:28317000-28318200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:28317000-28318200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr6:28317000-28318200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:28317000-28318200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:28317000-28318200	Active TSS	Brain Germinal Matrix	brain
10	chr6:28317000-28318200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:28317000-28318200	Active TSS	Fetal Lung	lung
12	chr6:28317000-28318200	Active TSS	HMEC	breast
13	chr6:28317000-28318200	Active TSS	NHEK	skin
14	chr6:28317000-28318400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:28317000-28318400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:28317000-28318400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:28317000-28318400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:28317000-28318800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:28317000-28319000	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:28317000-28319000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr6:28317200-28317600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:28317200-28317600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:28317200-28317600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr6:28317200-28317600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr6:28317200-28317600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:28317200-28317600	Bivalent/Poised TSS	Fetal Brain Female	brain
27	chr6:28317200-28317600	Flanking Active TSS	HUVEC	blood vessel
28	chr6:28317200-28317800	Active TSS	Primary T cells fromperipheralblood	blood
29	chr6:28317200-28317800	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr6:28317200-28318000	Active TSS	Primary B cells from peripheral blood	blood
31	chr6:28317200-28318000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:28317200-28318000	Active TSS	Brain Angular Gyrus	brain
33	chr6:28317200-28318000	Active TSS	Duodenum Mucosa	Duodenum
34	chr6:28317200-28318000	Active TSS	Fetal Thymus	thymus
35	chr6:28317200-28318200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:28317200-28318200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr6:28317200-28318200	Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:28317200-28318200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:28317200-28318200	Active TSS	Brain Hippocampus Middle	brain
40	chr6:28317200-28318200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:28317200-28318200	Active TSS	Brain Substantia Nigra	brain
42	chr6:28317200-28318200	Active TSS	Colon Smooth Muscle	Colon
43	chr6:28317200-28318200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr6:28317200-28318200	Active TSS	Fetal Brain Male	brain
45	chr6:28317200-28318200	Active TSS	Fetal Muscle Leg	muscle
46	chr6:28317200-28318200	Active TSS	Psoas Muscle	Psoas
47	chr6:28317200-28318200	Active TSS	Right Ventricle	heart
48	chr6:28317200-28318200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr6:28317200-28318200	Active TSS	Thymus	Thymus
50	chr6:28317200-28318200	Active TSS	Hela-S3	cervix

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