Variant report

Variant	rs540011481
Chromosome Location	chr7:3340266-3340267
allele	G/T
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	RAD21	chr7:3340160-3340979	MCF-7	breast:	n/a	n/a
2	MAX	chr7:3340236-3341061	HCT-116	colon:	n/a	chr7:3340556-3340566
3	CTCF	chr7:3339276-3341235	SK-N-SH	brain:	n/a	chr7:3339295-3339303 chr7:3340483-3340496 chr7:3339382-3339390
4	EP300	chr7:3340260-3341049	SK-N-SH	brain:	n/a	chr7:3340459-3340475 chr7:3340748-3340757 chr7:3340695-3340704 chr7:3340638-3340647 chr7:3340735-3340751
5	POLR2A	chr7:3340214-3341121	MCF-7	breast:	n/a	n/a
6	CTCF	chr7:3340179-3341039	A549	lung:	n/a	chr7:3340483-3340496
7	SIN3AK20	chr7:3339879-3341185	PANC-1	pancreas:	n/a	n/a
8	RAD21	chr7:3340235-3340997	IMR90	lung:	n/a	n/a
9	SMC3	chr7:3339220-3341228	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr7:3339844-3341257	MCF-7	breast:	n/a	n/a
11	MAX	chr7:3339896-3341192	HepG2	liver:	n/a	chr7:3340556-3340566
12	YY1	chr7:3340179-3340786	GM12878	blood:	n/a	chr7:3340750-3340759 chr7:3340664-3340678 chr7:3340464-3340475 chr7:3340661-3340675 chr7:3340745-3340759 chr7:3340666-3340675
13	CTCF	chr7:3340240-3340390	HBMEC	blood vessel:	n/a	n/a
14	MXI1	chr7:3339463-3341267	SK-N-SH	brain:	n/a	n/a
15	BACH1	chr7:3339959-3340991	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr7:3340254-3340864	PANC-1	pancreas:	n/a	n/a
17	REST	chr7:3340181-3340978	H1-neurons	neurons:	n/a	chr7:3340529-3340542 chr7:3340520-3340533
18	YY1	chr7:3340174-3340818	SK-N-SH_RA	brain:	n/a	chr7:3340750-3340759 chr7:3340664-3340678 chr7:3340464-3340475 chr7:3340661-3340675 chr7:3340745-3340759 chr7:3340666-3340675
19	MAX	chr7:3340228-3341052	ECC-1	luminal epithelium:	n/a	chr7:3340556-3340566
20	YY1	chr7:3340232-3340873	SK-N-SH_RA	brain:	n/a	chr7:3340750-3340759 chr7:3340664-3340678 chr7:3340464-3340475 chr7:3340661-3340675 chr7:3340745-3340759 chr7:3340666-3340675
21	MAX	chr7:3339949-3341060	HepG2	liver:	n/a	chr7:3340556-3340566
22	E2F6	chr7:3340211-3341039	A549	lung:	n/a	chr7:3340661-3340671 chr7:3340635-3340645 chr7:3340638-3340647 chr7:3340765-3340774 chr7:3340640-3340652 chr7:3340748-3340758 chr7:3340731-3340740 chr7:3340437-3340451 chr7:3340641-3340652 chr7:3340557-3340566 chr7:3340695-3340705
23	MAZ	chr7:3340237-3341140	IMR90	lung:	n/a	chr7:3340556-3340566
24	CTCF	chr7:3340240-3340390	SAEC	small airway:	n/a	n/a
25	MAX	chr7:3340024-3341114	A549	lung:	n/a	chr7:3340556-3340566
26	MAX	chr7:3339823-3341087	MCF-7	breast:	n/a	chr7:3340556-3340566
27	CREB1	chr7:3340132-3341053	A549	lung:	n/a	n/a
28	MAX	chr7:3339893-3341102	HepG2	liver:	n/a	chr7:3340556-3340566
29	CTCF	chr7:3340260-3340410	HCPEpiC	choroid plexus:	n/a	n/a
30	RAD21	chr7:3340218-3340936	A549	lung:	n/a	n/a
31	CTCF	chr7:3340140-3340290	NHEK	skin:	n/a	n/a
32	MAX	chr7:3340220-3341053	A549	lung:	n/a	chr7:3340556-3340566
33	HA-E2F1	chr7:3340140-3341041	MCF-7	breast:	n/a	chr7:3340661-3340671 chr7:3340635-3340645 chr7:3340638-3340647 chr7:3340765-3340774 chr7:3340640-3340652 chr7:3340748-3340758 chr7:3340731-3340740 chr7:3340437-3340451 chr7:3340557-3340566 chr7:3340695-3340705
34	HDAC2	chr7:3340238-3340782	HepG2	liver:	n/a	n/a
35	CTCF	chr7:3340220-3340370	GM12869	blood:	n/a	n/a
36	MAX	chr7:3340231-3341082	MCF-7	breast:	n/a	chr7:3340556-3340566
37	RAD21	chr7:3339138-3341287	SK-N-SH	brain:	n/a	chr7:3339313-3339327 chr7:3339322-3339335
38	MYC	chr7:3340130-3341001	A549	lung:	n/a	chr7:3340556-3340566
39	YY1	chr7:3340186-3340555	H1-hESC	embryonic stem cell:	n/a	chr7:3340464-3340475
40	CTCF	chr7:3340260-3340410	A549	lung:	n/a	n/a
41	SIN3A	chr7:3340224-3341022	H1-hESC	embryonic stem cell:	n/a	n/a
42	EP300	chr7:3340262-3341039	ECC-1	luminal epithelium:	n/a	chr7:3340459-3340475 chr7:3340748-3340757 chr7:3340695-3340704 chr7:3340638-3340647 chr7:3340735-3340751
43	E2F6	chr7:3340198-3340923	H1-hESC	embryonic stem cell:	n/a	chr7:3340661-3340671 chr7:3340635-3340645 chr7:3340638-3340647 chr7:3340765-3340774 chr7:3340640-3340652 chr7:3340748-3340758 chr7:3340731-3340740 chr7:3340437-3340451 chr7:3340641-3340652 chr7:3340557-3340566 chr7:3340695-3340705
44	CTCF	chr7:3340240-3340450	AG09319	gingival:	n/a	n/a
45	MAX	chr7:3340248-3341112	ECC-1	luminal epithelium:	n/a	chr7:3340556-3340566
46	HDAC2	chr7:3340091-3340976	MCF-7	breast:	n/a	n/a
47	ZNF263	chr7:3339425-3341047	HEK293-T-REx	kidney:	n/a	n/a
48	CTCF	chr7:3340260-3340410	HBMEC	blood vessel:	n/a	n/a
49	FOXA2	chr7:3340215-3341006	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:3340063..3340822-chr7:3439252..3440083,5	MCF-7	breast:
2	chr7:3339718..3341766-chr7:3458306..3459954,2	K562	blood:
3	chr7:3194510..3195232-chr7:3340158..3340723,2	MCF-7	breast:
4	chr7:3250247..3250807-chr7:3340190..3341077,3	MCF-7	breast:

Variant related genes	Relation type
SDK1	TF binding region
ENSG00000211544	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv1803572	chr7:3327994-3341589	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv605885	chr7:3337081-3340551	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv19885	chr7:3339551-3341631	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv3328363	chr7:3339726-3342349	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv3345863	chr7:3339851-3342399	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv1802865	chr7:3339987-3341589	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv605886	chr7:3340090-3340969	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv605887	chr7:3340187-3341488	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv1803913	chr7:3340187-3341589	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	esv1836877	chr7:3340187-3341589	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv605888	chr7:3340187-3341589	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv605889	chr7:3340187-3342276	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3339400-3340600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr7:3339400-3340600	Bivalent Enhancer	Placenta	Placenta
3	chr7:3339600-3342600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr7:3339800-3340400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
5	chr7:3339800-3340400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:3339800-3340400	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:3339800-3340400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:3339800-3340400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:3339800-3340400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:3339800-3340400	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr7:3339800-3340600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr7:3339800-3340600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr7:3339800-3340600	Active TSS	Brain Substantia Nigra	brain
14	chr7:3339800-3340600	Enhancers	Fetal Brain Male	brain
15	chr7:3339800-3341600	Active TSS	Fetal Brain Female	brain
16	chr7:3339800-3342200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:3339800-3342200	Active TSS	HSMMtube	muscle
18	chr7:3340000-3340400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:3340000-3340400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr7:3340000-3340400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:3340000-3340400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr7:3340000-3340400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr7:3340000-3340400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr7:3340000-3340400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr7:3340000-3340400	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr7:3340000-3340400	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr7:3340000-3340400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr7:3340000-3340400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:3340000-3340400	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr7:3340000-3340400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr7:3340000-3340400	Enhancers	Fetal Heart	heart
32	chr7:3340000-3340400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
33	chr7:3340000-3340400	Enhancers	Gastric	stomach
34	chr7:3340000-3340400	Flanking Active TSS	Left Ventricle	heart
35	chr7:3340000-3340400	Enhancers	Lung	lung
36	chr7:3340000-3340400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
37	chr7:3340000-3340400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
38	chr7:3340000-3340400	Enhancers	Spleen	Spleen
39	chr7:3340000-3340600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:3340000-3340600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr7:3340000-3340600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr7:3340000-3340600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr7:3340000-3340600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr7:3340000-3340600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:3340000-3340600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr7:3340000-3340600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:3340000-3340600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr7:3340000-3340600	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr7:3340000-3340600	Flanking Active TSS	Colonic Mucosa	Colon
50	chr7:3340000-3340600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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