Variant report

Variant	rs4946722
Chromosome Location	chr6:106532446-106532447
allele	A/C
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	SMC3	chr6:106532315-106532898	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:106532411-106536250	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr6:106532176-106532958	NB4	blood:	n/a	n/a
4	RAD21	chr6:106532184-106532921	GM12878	blood:	n/a	n/a
5	MAFF	chr6:106532360-106532738	HepG2	liver:	n/a	chr6:106532545-106532559 chr6:106532546-106532564
6	CEBPB	chr6:106532247-106532931	IMR90	lung:	n/a	n/a
7	SPI1	chr6:106531900-106532953	GM12878	blood:	n/a	chr6:106532453-106532462 chr6:106532862-106532875 chr6:106532689-106532696 chr6:106532688-106532697 chr6:106532447-106532460
8	MAX	chr6:106532328-106533109	NB4	blood:	n/a	n/a
9	FOS	chr6:106532308-106533152	MCF10A-Er-Src	breast:	n/a	chr6:106532547-106532557 chr6:106532394-106532402
10	ZMIZ1	chr6:106532386-106532863	K562	blood:	n/a	n/a
11	RCOR1	chr6:106532363-106532866	K562	blood:	n/a	n/a
12	E2F4	chr6:106532423-106532994	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr6:106532300-106532450	HEEpiC	esophagus:	n/a	n/a
14	FOXM1	chr6:106532138-106532811	GM12878	blood:	n/a	n/a
15	SPI1	chr6:106532296-106532582	K562	blood:	n/a	chr6:106532453-106532462 chr6:106532447-106532460
16	SETDB1	chr6:106532355-106533045	U2OS	brain:	n/a	n/a
17	CEBPB	chr6:106532429-106532997	K562	blood:	n/a	n/a
18	EP300	chr6:106532146-106533103	GM12878	blood:	n/a	chr6:106532233-106532247 chr6:106532448-106532462 chr6:106532978-106532992
19	TCF12	chr6:106531788-106532874	SK-N-SH	brain:	n/a	chr6:106532153-106532160
20	RAD21	chr6:106532376-106532873	H1-hESC	embryonic stem cell:	n/a	n/a
21	TBL1XR1	chr6:106532240-106533119	GM12878	blood:	n/a	n/a
22	RFX5	chr6:106532387-106532619	HepG2	liver:	n/a	n/a
23	PAX5	chr6:106532286-106532570	GM12878	blood:	n/a	chr6:106532453-106532462
24	TCF12	chr6:106532301-106532796	GM12878	blood:	n/a	n/a
25	CEBPB	chr6:106532349-106533140	HCT-116	colon:	n/a	n/a
26	FOSL2	chr6:106532141-106532936	A549	lung:	n/a	chr6:106532547-106532557 chr6:106532394-106532402
27	PAX5	chr6:106532300-106532592	GM12878	blood:	n/a	chr6:106532453-106532462
28	SPI1	chr6:106532194-106532701	GM12878	blood:	n/a	chr6:106532453-106532462 chr6:106532689-106532696 chr6:106532688-106532697 chr6:106532447-106532460
29	BHLHE40	chr6:106532307-106533242	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:106532311-106532703	GM12878	blood:	n/a	n/a
31	TCF12	chr6:106532309-106532657	GM12878	blood:	n/a	n/a
32	KAP1	chr6:106532223-106534355	U2OS	brain:	n/a	chr6:106532392-106532401
33	MAFK	chr6:106532210-106532889	IMR90	lung:	n/a	chr6:106532544-106532560 chr6:106532549-106532558 chr6:106532548-106532558 chr6:106532546-106532555 chr6:106532541-106532557 chr6:106532541-106532556 chr6:106532542-106532562 chr6:106532545-106532559
34	CEBPB	chr6:106532365-106534389	Hela-S3	cervix:	n/a	chr6:106534041-106534058
35	MTA3	chr6:106532166-106532726	GM12878	blood:	n/a	n/a
36	CHD2	chr6:106532121-106532879	GM12878	blood:	n/a	n/a
37	IRF1	chr6:106532374-106532936	K562	blood:	n/a	chr6:106532452-106532461 chr6:106532449-106532463 chr6:106532453-106532463
38	CEBPB	chr6:106532347-106533044	A549	lung:	n/a	n/a
39	SMC3	chr6:106532342-106534811	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr6:106532375-106532902	SK-N-SH_RA	brain:	n/a	n/a
41	RUNX3	chr6:106532202-106532700	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:106532295-106532922	GM12878	blood:	n/a	n/a
43	ATF2	chr6:106532169-106532735	GM12878	blood:	n/a	n/a
44	MAFK	chr6:106532367-106532798	HepG2	liver:	n/a	chr6:106532544-106532560 chr6:106532549-106532558 chr6:106532548-106532558 chr6:106532546-106532555 chr6:106532541-106532557 chr6:106532541-106532556 chr6:106532542-106532562 chr6:106532545-106532559
45	RAD21	chr6:106532304-106532922	IMR90	lung:	n/a	n/a
46	RAD21	chr6:106532331-106532911	A549	lung:	n/a	n/a
47	SPI1	chr6:106532191-106532712	HL-60	blood:	n/a	chr6:106532453-106532462 chr6:106532689-106532696 chr6:106532688-106532697 chr6:106532447-106532460
48	CTCF	chr6:106532440-106532945	K562	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
49	POU2F2	chr6:106532213-106532860	GM12878	blood:	n/a	n/a
50	CTCF	chr6:106532444-106532983	K562	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785

No.	Distal block	Cell Line	Cell type
1	chr6:106525524..106527475-chr6:106529699..106532511,2	K562	blood:
2	chr6:106240681..106241704-chr6:106532154..106532860,3	MCF-7	breast:
3	chr6:106181700..106182227-chr6:106532304..106533098,2	MCF-7	breast:
4	chr6:106528913..106530600-chr6:106531413..106534036,2	MCF-7	breast:

Variant related genes	Relation type
PRDM1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1010273	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12175062	0.91[CEU][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1934593	0.91[CEU][hapmap]
rs1985899	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3804333	1.00[LWK][hapmap]
rs3827644	1.00[LWK][hapmap]
rs4946724	0.81[CEU][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4946725	0.81[CEU][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9373832	0.84[EUR][1000 genomes]
rs9373839	1.00[LWK][hapmap]
rs9386508	1.00[ASW][hapmap]
rs9386509	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106528600-106532600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:106528800-106533600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:106529800-106533000	Enhancers	NHLF	lung
4	chr6:106529800-106534000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:106530000-106533200	Enhancers	NHEK	skin
6	chr6:106530200-106533800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:106530400-106533000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:106530400-106533200	Enhancers	HMEC	breast
9	chr6:106530400-106533200	Enhancers	NH-A	brain
10	chr6:106530400-106533200	Enhancers	Osteobl	bone
11	chr6:106530400-106533400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:106530400-106533800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:106530600-106533200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:106530600-106533200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:106530600-106533400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:106530600-106533400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:106530600-106533400	Enhancers	HSMM	muscle
18	chr6:106530600-106533600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:106530600-106533800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr6:106530600-106533800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:106530600-106533800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:106530600-106533800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:106530800-106533000	Enhancers	A549	lung
24	chr6:106530800-106533200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:106530800-106533800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:106531000-106532600	Weak transcription	Ovary	ovary
27	chr6:106531000-106533600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:106531200-106533400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:106531200-106533400	Weak transcription	Psoas Muscle	Psoas
30	chr6:106531400-106533400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr6:106531600-106533200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:106531600-106533600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:106531600-106533600	Enhancers	Primary T cells from cord blood	blood
34	chr6:106531600-106534000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:106531800-106532800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr6:106531800-106533000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:106531800-106533400	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:106532000-106532800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:106532000-106532800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:106532000-106532800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr6:106532000-106532800	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr6:106532000-106532800	Flanking Active TSS	GM12878-XiMat	blood
43	chr6:106532000-106532800	Flanking Active TSS	NHDF-Ad	bronchial
44	chr6:106532000-106533200	Enhancers	Hela-S3	cervix
45	chr6:106532000-106533400	Enhancers	Duodenum Mucosa	Duodenum
46	chr6:106532000-106533400	Enhancers	HSMMtube	muscle
47	chr6:106532000-106533600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:106532000-106533800	Enhancers	Primary B cells from peripheral blood	blood
49	chr6:106532000-106533800	Bivalent Enhancer	Fetal Thymus	thymus
50	chr6:106532000-106533800	Enhancers	K562	blood

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