Variant report

Variant	rs9472662
Chromosome Location	chr6:45982976-45982977
allele	A/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	CTCF	chr6:45982944-45983184	MCF-7	breast:	n/a	chr6:45983169-45983182 chr6:45983015-45983028 chr6:45983169-45983182 chr6:45983153-45983162
2	EGR1	chr6:45982880-45983067	K562	blood:	n/a	chr6:45982973-45982986
3	CTCF	chr6:45982960-45983110	GM12869	blood:	n/a	chr6:45983015-45983028
4	MAX	chr6:45982742-45983568	ECC-1	luminal epithelium:	n/a	chr6:45983492-45983502
5	EGR1	chr6:45982641-45983850	HCT-116	colon:	n/a	chr6:45983638-45983648 chr6:45983491-45983501 chr6:45982973-45982986 chr6:45983486-45983499
6	CTCF	chr6:45982880-45983030	HRE	kidney:	n/a	chr6:45983015-45983028
7	CTCF	chr6:45982941-45983126	MCF-7	breast:	n/a	chr6:45983015-45983028
8	ZBTB7A	chr6:45982816-45983894	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr6:45982920-45983070	HepG2	liver:	n/a	chr6:45983015-45983028
10	TCF12	chr6:45982753-45983476	ECC-1	luminal epithelium:	n/a	chr6:45982887-45982894 chr6:45983186-45983193
11	CTCF	chr6:45982920-45983070	HEK293	kidney:	n/a	chr6:45983015-45983028
12	CTCF	chr6:45982940-45983090	Caco-2	colon:	n/a	chr6:45983015-45983028
13	MAX	chr6:45982696-45983439	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr6:45982937-45983133	GM19239	blood:	n/a	chr6:45983015-45983028
15	POLR2A	chr6:45982968-45983115	MCF-7	breast:	n/a	n/a
16	CTCF	chr6:45982961-45983098	GM12891	blood:	n/a	chr6:45983015-45983028
17	E2F6	chr6:45982941-45983102	K562	blood:	n/a	chr6:45982966-45982975
18	CTCF	chr6:45982963-45983127	GM19240	blood:	n/a	chr6:45983015-45983028
19	SIN3A	chr6:45982166-45983671	H1-hESC	embryonic stem cell:	n/a	chr6:45983330-45983339 chr6:45983069-45983082 chr6:45983635-45983646 chr6:45983359-45983372 chr6:45983329-45983343
20	CTCF	chr6:45982955-45983069	GM12878	blood:	n/a	chr6:45983015-45983028
21	MYC	chr6:45982966-45983094	MCF-7	breast:	n/a	n/a
22	ZBTB7A	chr6:45982812-45983917	ECC-1	luminal epithelium:	n/a	n/a
23	TCF12	chr6:45982733-45983649	ECC-1	luminal epithelium:	n/a	chr6:45982887-45982894 chr6:45983186-45983193
24	YY1	chr6:45982839-45983279	ECC-1	luminal epithelium:	n/a	chr6:45983109-45983118
25	HDAC2	chr6:45982852-45983558	MCF-7	breast:	n/a	chr6:45983329-45983348
26	MYC	chr6:45982965-45983009	MCF-7	breast:	n/a	n/a
27	EGR1	chr6:45982773-45983206	ECC-1	luminal epithelium:	n/a	chr6:45982973-45982986
28	ZNF263	chr6:45981948-45983628	HEK293-T-REx	kidney:	n/a	chr6:45982829-45982838 chr6:45983486-45983495 chr6:45982539-45982560
29	EP300	chr6:45982734-45983833	ECC-1	luminal epithelium:	n/a	chr6:45983632-45983648 chr6:45982770-45982784 chr6:45983359-45983375 chr6:45982746-45982760 chr6:45983109-45983125
30	CTCF	chr6:45982940-45983090	SAEC	small airway:	n/a	chr6:45983015-45983028
31	EGR1	chr6:45982767-45983288	HCT-116	colon:	n/a	chr6:45982973-45982986
32	ELF1	chr6:45982809-45983186	GM12878	blood:	n/a	n/a
33	CTCF	chr6:45982954-45982995	Pancreas_OC	pancreas:	n/a	n/a
34	CTCF	chr6:45982966-45983108	GM19238	blood:	n/a	chr6:45983015-45983028
35	EGR1	chr6:45982761-45983191	ECC-1	luminal epithelium:	n/a	chr6:45982973-45982986
36	CTBP2	chr6:45982874-45984194	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:45982943-45983117	MCF-7	breast:	n/a	chr6:45983015-45983028
38	HMGN3	chr6:45982951-45983138	K562	blood:	n/a	n/a
39	CTCF	chr6:45982940-45983090	WERI-Rb-1	eye:	n/a	chr6:45983015-45983028
40	TEAD4	chr6:45982751-45983207	ECC-1	luminal epithelium:	n/a	n/a
41	CTCF	chr6:45982960-45983110	GM06990	blood:	n/a	chr6:45983015-45983028
42	CTCF	chr6:45982860-45983110	WERI-Rb-1	eye:	n/a	chr6:45983015-45983028
43	CTCF	chr6:45982920-45983070	Caco-2	colon:	n/a	chr6:45983015-45983028
44	CTCF	chr6:45982920-45983070	SAEC	small airway:	n/a	chr6:45983015-45983028
45	POLR2A	chr6:45982899-45983165	ECC-1	luminal epithelium:	n/a	n/a
46	EGR1	chr6:45982854-45983089	K562	blood:	n/a	chr6:45982973-45982986

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45980539..45983062-chr6:45983993..45986730,2	K562	blood:

Variant related genes	Relation type
RNU6-754P	TF binding region
ENSG00000212468	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10484840	1.00[JPT][hapmap]
rs13328271	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1578005	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2179993	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2179994	0.91[LWK][hapmap]
rs3777597	1.00[JPT][hapmap]
rs59238881	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6906803	0.93[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6919720	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6921481	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6922977	1.00[JPT][hapmap]
rs6927513	1.00[JPT][hapmap]
rs6936849	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7771759	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9296477	1.00[JPT][hapmap]
rs9463167	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9463170	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9463172	0.89[LWK][hapmap]
rs9472661	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9472666	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9472667	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs9472670	1.00[JPT][hapmap]
rs9472674	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv885867	chr6:45936223-45982976	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1025846	chr6:45955173-46047269	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9472662	NFKBIE	cis	cerebellum	SCAN
rs9472662	SPATS1	cis	parietal	SCAN
rs9472662	UBR2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45979200-45984000	Active TSS	Right Atrium	heart
2	chr6:45980200-45983800	Active TSS	Fetal Kidney	kidney
3	chr6:45980800-45983800	Active TSS	Small Intestine	intestine
4	chr6:45980800-45984000	Active TSS	Left Ventricle	heart
5	chr6:45981200-45984000	Active TSS	Right Ventricle	heart
6	chr6:45981600-45983000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr6:45981800-45983800	Active TSS	Lung	lung
8	chr6:45981800-45983800	Active TSS	Psoas Muscle	Psoas
9	chr6:45981800-45984600	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr6:45982000-45983600	Active TSS	Fetal Heart	heart
11	chr6:45982000-45983800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:45982000-45984200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:45982200-45983000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr6:45982200-45983000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr6:45982200-45983000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:45982200-45983000	Active TSS	Brain Substantia Nigra	brain
17	chr6:45982200-45983000	Flanking Bivalent TSS/Enh	Placenta	Placenta
18	chr6:45982200-45983000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
19	chr6:45982200-45983200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:45982200-45983800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:45982200-45983800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr6:45982200-45983800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr6:45982200-45983800	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr6:45982200-45983800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:45982400-45983000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
26	chr6:45982400-45983000	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr6:45982400-45983200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
28	chr6:45982400-45983200	Flanking Bivalent TSS/Enh	NH-A	brain
29	chr6:45982400-45983400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr6:45982400-45983400	Active TSS	Aorta	Aorta
31	chr6:45982400-45983600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr6:45982400-45983600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:45982400-45983600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:45982400-45983600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
35	chr6:45982400-45983600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr6:45982400-45983600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
37	chr6:45982400-45983600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
38	chr6:45982400-45983600	Bivalent/Poised TSS	Thymus	Thymus
39	chr6:45982400-45983800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr6:45982400-45983800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:45982400-45983800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:45982400-45983800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
43	chr6:45982400-45983800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
44	chr6:45982400-45983800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:45982400-45984200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:45982400-45984200	Bivalent/Poised TSS	Fetal Lung	lung
47	chr6:45982400-45984400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:45982600-45983000	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr6:45982600-45983000	Active TSS	Colon Smooth Muscle	Colon
50	chr6:45982600-45983000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum

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