Variant report

Variant	rs2817040
Chromosome Location	chr6:35705606-35705607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:143)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:143 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:35705327-35705671	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr6:35705318-35705777	ECC-1	luminal epithelium:	n/a	chr6:35705526-35705537
3	CEBPB	chr6:35705313-35705702	ECC-1	luminal epithelium:	n/a	chr6:35705526-35705537
4	CEBPB	chr6:35705303-35705874	HepG2	liver:	n/a	chr6:35705526-35705537
5	MAFF	chr6:35705344-35705640	HepG2	liver:	n/a	n/a
6	ZNF143	chr6:35705298-35705690	K562	blood:	n/a	n/a
7	CTCF	chr6:35705248-35705781	HCT-116	colon:	n/a	n/a
8	RAD21	chr6:35705231-35705612	GM12878	blood:	n/a	n/a
9	MYC	chr6:35705277-35705678	NB4	blood:	n/a	n/a
10	MAFK	chr6:35705223-35705767	K562	blood:	n/a	n/a
11	CTCF	chr6:35705323-35705684	A549	lung:	n/a	n/a
12	MAZ	chr6:35705307-35705728	K562	blood:	n/a	n/a
13	MYC	chr6:35705286-35705679	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr6:35705338-35705623	T-47D	breast:	n/a	n/a
15	STAT3	chr6:35705351-35705647	MCF10A-Er-Src	breast:	n/a	n/a
16	MAZ	chr6:35705332-35705607	GM12878	blood:	n/a	n/a
17	CEBPB	chr6:35705346-35705684	K562	blood:	n/a	chr6:35705526-35705537
18	YY1	chr6:35705417-35705797	ECC-1	luminal epithelium:	n/a	n/a
19	CTCF	chr6:35705362-35705667	GM12878	blood:	n/a	n/a
20	CTCF	chr6:35705390-35705608	MCF-7	breast:	n/a	n/a
21	RAD21	chr6:35705032-35705943	HCT-116	colon:	n/a	n/a
22	CTCF	chr6:35705352-35705631	Pancreas_OC	pancreas:	n/a	n/a
23	SMC3	chr6:35705194-35705700	HepG2	liver:	n/a	n/a
24	FOS	chr6:35705354-35705647	MCF10A-Er-Src	breast:	n/a	n/a
25	RAD21	chr6:35705334-35705674	A549	lung:	n/a	n/a
26	JUN	chr6:35705357-35705675	HepG2	liver:	n/a	chr6:35705523-35705536
27	ATF3	chr6:35705401-35705659	HepG2	liver:	n/a	n/a
28	CEBPB	chr6:35705362-35705646	HepG2	liver:	n/a	chr6:35705526-35705537
29	CTCF	chr6:35705212-35705816	MCF-7	breast:	n/a	n/a
30	CTCF	chr6:35705354-35705645	MCF-7	breast:	n/a	n/a
31	CTCF	chr6:35705229-35705719	GM12878	blood:	n/a	n/a
32	MAX	chr6:35705258-35705715	NB4	blood:	n/a	n/a
33	RAD21	chr6:35704697-35705924	SK-N-SH	brain:	n/a	n/a
34	YY1	chr6:35705305-35705643	SK-N-SH_RA	brain:	n/a	n/a
35	EP300	chr6:35705359-35705674	HepG2	liver:	n/a	chr6:35705523-35705537
36	CTCF	chr6:35705460-35705610	RPTEC	kidney:	n/a	n/a
37	MAFK	chr6:35705258-35705655	HepG2	liver:	n/a	n/a
38	CTCF	chr6:35705347-35705664	Medullo	brain:	n/a	n/a
39	CTCF	chr6:35704715-35705974	SK-N-SH	brain:	n/a	n/a
40	CTCF	chr6:35705237-35705699	HepG2	liver:	n/a	n/a
41	YY1	chr6:35705301-35705745	HepG2	liver:	n/a	n/a
42	CTCF	chr6:35705205-35705708	IMR90	lung:	n/a	n/a
43	CTCF	chr6:35705460-35705610	A549	lung:	n/a	n/a
44	MYC	chr6:35705294-35705719	K562	blood:	n/a	n/a
45	MAFK	chr6:35705314-35705632	HepG2	liver:	n/a	n/a
46	CEBPB	chr6:35705158-35705918	HCT-116	colon:	n/a	chr6:35705526-35705537
47	CEBPB	chr6:35705316-35705617	A549	lung:	n/a	chr6:35705526-35705537
48	CTCF	chr6:35705334-35705631	Kidney_OC	kidney:	n/a	n/a
49	RAD21	chr6:35705257-35705676	H1-hESC	embryonic stem cell:	n/a	n/a
50	CEBPB	chr6:35705350-35705974	MCF-7	breast:	n/a	chr6:35705526-35705537

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35309893..35310744-chr6:35704999..35705946,2	K562	blood:
2	chr6:35434775..35437842-chr6:35701549..35705876,5	MCF-7	breast:
3	chr6:35635609..35637648-chr6:35705091..35708363,3	K562	blood:
4	chr6:35265403..35265941-chr6:35705093..35706000,2	MCF-7	breast:
5	chr6:35536496..35537201-chr6:35705517..35706230,2	MCF-7	breast:
6	chr6:35551333..35552161-chr6:35705001..35705965,6	MCF-7	breast:
7	chr6:35654784..35658036-chr6:35702203..35706321,5	MCF-7	breast:
8	chr6:35511057..35513907-chr6:35704750..35707121,2	K562	blood:
9	chr6:35465886..35468037-chr6:35705048..35706925,2	K562	blood:
10	chr6:35551241..35552671-chr6:35704972..35706000,16	K562	blood:
11	chr6:35490540..35491130-chr6:35705031..35706454,3	MCF-7	breast:
12	chr6:35265059..35266000-chr6:35705022..35705927,2	K562	blood:
13	chr6:35433822..35437754-chr6:35703135..35706478,6	K562	blood:
14	chr6:35654156..35657013-chr6:35704693..35707749,4	K562	blood:
15	chr6:35695421..35696970-chr6:35705398..35706978,2	MCF-7	breast:
16	chr6:35551377..35552255-chr6:35705016..35705834,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232909	TF binding region
ENSG00000096060	Chromatin interaction
ENSG00000198755	Chromatin interaction
ENSG00000023892	Chromatin interaction
ENSG00000228559	Chromatin interaction
ENSG00000112033	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2766536	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817032	0.84[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2817035	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4236047	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1028947	chr6:35670521-35714541	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv885805	chr6:35685955-35779879	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2817040	SRPK1	cis	parietal	SCAN
rs2817040	RNF8	cis	parietal	SCAN
rs2817040	BRPF3	cis	cerebellum	SCAN
rs2817040	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35700200-35706000	Enhancers	Pancreas	Pancrea
2	chr6:35700400-35706000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:35700600-35705800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:35700600-35705800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:35700600-35705800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr6:35700600-35705800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:35700600-35706000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:35700600-35706400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:35700600-35707200	Weak transcription	Fetal Intestine Small	intestine
10	chr6:35700600-35708000	Weak transcription	Fetal Brain Female	brain
11	chr6:35700800-35707400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:35700800-35710400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:35701200-35705800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:35701200-35706000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:35701800-35707600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:35702000-35707400	Weak transcription	Liver	Liver
17	chr6:35702400-35705800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:35703000-35705800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:35703000-35706000	Enhancers	Spleen	Spleen
20	chr6:35703000-35707800	Weak transcription	Stomach Mucosa	stomach
21	chr6:35703200-35705800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr6:35703200-35705800	Enhancers	Stomach Smooth Muscle	stomach
23	chr6:35703200-35706000	Enhancers	Lung	lung
24	chr6:35703400-35705800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:35703800-35705800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:35703800-35706400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:35703800-35707400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:35704000-35705800	Enhancers	Fetal Heart	heart
29	chr6:35704000-35705800	Enhancers	Right Ventricle	heart
30	chr6:35704200-35706000	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr6:35704200-35706200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:35704200-35707600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:35704200-35707600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:35704400-35707600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:35704400-35707600	Weak transcription	Fetal Stomach	stomach
36	chr6:35704600-35705800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:35704800-35705800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:35704800-35705800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr6:35704800-35706000	Enhancers	Left Ventricle	heart
40	chr6:35704800-35707200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:35705000-35705800	Enhancers	Brain Substantia Nigra	brain
42	chr6:35705000-35705800	Enhancers	Colon Smooth Muscle	Colon
43	chr6:35705000-35705800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:35705000-35705800	Enhancers	Fetal Brain Male	brain
45	chr6:35705000-35705800	Enhancers	Ovary	ovary
46	chr6:35705000-35706000	Enhancers	Fetal Muscle Trunk	muscle
47	chr6:35705000-35706400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr6:35705000-35706400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:35705000-35708000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:35705000-35709000	Enhancers	Cortex derived primary cultured neurospheres	brain

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