Variant report

Variant	rs1340064
Chromosome Location	chr6:106532658-106532659
allele	C/G
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	CTCF	chr6:106532638-106532832	MCF-7	breast:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
3	CTCF	chr6:106532620-106532770	GM12875	blood:	n/a	n/a
4	CTCF	chr6:106532620-106532770	HBMEC	blood vessel:	n/a	n/a
5	POLR2A	chr6:106532411-106536250	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr6:106532608-106532851	H1-hESC	embryonic stem cell:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
7	MYC	chr6:106532176-106532958	NB4	blood:	n/a	n/a
8	CTCF	chr6:106532640-106532790	GM12878	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
9	RAD21	chr6:106532184-106532921	GM12878	blood:	n/a	n/a
10	CTCF	chr6:106532640-106532790	GM12801	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
11	MAFF	chr6:106532360-106532738	HepG2	liver:	n/a	chr6:106532545-106532559 chr6:106532546-106532564
12	YY1	chr6:106532616-106532848	HCT-116	colon:	n/a	n/a
13	CEBPB	chr6:106532247-106532931	IMR90	lung:	n/a	n/a
14	STAT3	chr6:106532642-106532985	MCF10A-Er-Src	breast:	n/a	chr6:106532862-106532874 chr6:106532838-106532849 chr6:106532864-106532876
15	SPI1	chr6:106531900-106532953	GM12878	blood:	n/a	chr6:106532453-106532462 chr6:106532862-106532875 chr6:106532689-106532696 chr6:106532688-106532697 chr6:106532447-106532460
16	CHD2	chr6:106532628-106534442	Hela-S3	cervix:	n/a	n/a
17	MAX	chr6:106532328-106533109	NB4	blood:	n/a	n/a
18	FOS	chr6:106532308-106533152	MCF10A-Er-Src	breast:	n/a	chr6:106532547-106532557 chr6:106532394-106532402
19	CTCF	chr6:106532487-106532873	A549	lung:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
20	ZMIZ1	chr6:106532386-106532863	K562	blood:	n/a	n/a
21	CTCF	chr6:106532640-106532790	HVMF	connective:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
22	RCOR1	chr6:106532363-106532866	K562	blood:	n/a	n/a
23	CTCF	chr6:106532452-106532950	K562	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
24	SMC3	chr6:106532464-106532874	K562	blood:	n/a	n/a
25	CTCF	chr6:106532640-106532790	NHEK	skin:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
26	CTCF	chr6:106532613-106532849	GM19240	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
27	CTCF	chr6:106532613-106532846	ProgFib	skin:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
28	E2F4	chr6:106532423-106532994	MCF10A-Er-Src	breast:	n/a	n/a
29	PAX5	chr6:106532603-106532840	GM12878	blood:	n/a	n/a
30	CTCF	chr6:106532600-106532750	GM12867	blood:	n/a	n/a
31	CTCF	chr6:106532597-106532859	Fibrobl	skin:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
32	NFYA	chr6:106532632-106532988	Hela-S3	cervix:	n/a	n/a
33	FOXM1	chr6:106532138-106532811	GM12878	blood:	n/a	n/a
34	CTCF	chr6:106532640-106532790	NB4	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
35	CTCF	chr6:106532600-106532750	HEEpiC	esophagus:	n/a	n/a
36	SETDB1	chr6:106532355-106533045	U2OS	brain:	n/a	n/a
37	CTCF	chr6:106532560-106532710	A549	lung:	n/a	n/a
38	WRNIP1	chr6:106532456-106533131	GM12878	blood:	n/a	n/a
39	RFX5	chr6:106532490-106532905	Hela-S3	cervix:	n/a	n/a
40	CEBPB	chr6:106532429-106532997	K562	blood:	n/a	n/a
41	MYC	chr6:106532511-106532933	K562	blood:	n/a	n/a
42	EP300	chr6:106532146-106533103	GM12878	blood:	n/a	chr6:106532233-106532247 chr6:106532448-106532462 chr6:106532978-106532992
43	TCF12	chr6:106531788-106532874	SK-N-SH	brain:	n/a	chr6:106532153-106532160
44	RAD21	chr6:106532376-106532873	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr6:106532640-106532790	GM12871	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
46	TBL1XR1	chr6:106532240-106533119	GM12878	blood:	n/a	n/a
47	CTCF	chr6:106532601-106532836	HepG2	liver:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
48	CTCF	chr6:106532580-106532730	GM12878	blood:	n/a	n/a
49	CTCF	chr6:106532598-106532869	GM19239	blood:	n/a	chr6:106532765-106532786 chr6:106532776-106532785
50	CTCF	chr6:106532640-106532790	HCT-116	colon:	n/a	chr6:106532765-106532786 chr6:106532776-106532785

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

Variant related genes	Relation type
PRDM1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12175062	0.81[JPT][hapmap]
rs1984224	0.82[ASN][1000 genomes]
rs4946724	0.81[JPT][hapmap]
rs6924535	0.83[CHB][hapmap];0.82[ASN][1000 genomes]

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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106528800-106533600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:106529800-106533000	Enhancers	NHLF	lung
3	chr6:106529800-106534000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:106530000-106533200	Enhancers	NHEK	skin
5	chr6:106530200-106533800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:106530400-106533000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:106530400-106533200	Enhancers	HMEC	breast
8	chr6:106530400-106533200	Enhancers	NH-A	brain
9	chr6:106530400-106533200	Enhancers	Osteobl	bone
10	chr6:106530400-106533400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:106530400-106533800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:106530600-106533200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:106530600-106533200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:106530600-106533400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:106530600-106533400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:106530600-106533400	Enhancers	HSMM	muscle
17	chr6:106530600-106533600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:106530600-106533800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:106530600-106533800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:106530600-106533800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:106530600-106533800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:106530800-106533000	Enhancers	A549	lung
23	chr6:106530800-106533200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:106530800-106533800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:106531000-106533600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:106531200-106533400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:106531200-106533400	Weak transcription	Psoas Muscle	Psoas
28	chr6:106531400-106533400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:106531600-106533200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:106531600-106533600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:106531600-106533600	Enhancers	Primary T cells from cord blood	blood
32	chr6:106531600-106534000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:106531800-106532800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr6:106531800-106533000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:106531800-106533400	Enhancers	Primary hematopoietic stem cells	blood
36	chr6:106532000-106532800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:106532000-106532800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:106532000-106532800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr6:106532000-106532800	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr6:106532000-106532800	Flanking Active TSS	GM12878-XiMat	blood
41	chr6:106532000-106532800	Flanking Active TSS	NHDF-Ad	bronchial
42	chr6:106532000-106533200	Enhancers	Hela-S3	cervix
43	chr6:106532000-106533400	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:106532000-106533400	Enhancers	HSMMtube	muscle
45	chr6:106532000-106533600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:106532000-106533800	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:106532000-106533800	Bivalent Enhancer	Fetal Thymus	thymus
48	chr6:106532000-106533800	Enhancers	K562	blood
49	chr6:106532000-106534000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr6:106532200-106533000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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