Variant report

Variant	rs539700909
Chromosome Location	chr7:3340622-3340623
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	MYC	chr7:3340453-3340653	MCF-7	breast:	n/a	chr7:3340556-3340566
2	CTCF	chr7:3340505-3340739	K562	blood:	n/a	n/a
3	CTCF	chr7:3340499-3340752	A549	lung:	n/a	n/a
4	CTCF	chr7:3340418-3340766	GM10266	blood:	n/a	chr7:3340483-3340496
5	YY1	chr7:3340430-3340933	ECC-1	luminal epithelium:	n/a	chr7:3340750-3340759 chr7:3340664-3340678 chr7:3340464-3340475 chr7:3340661-3340675 chr7:3340745-3340759 chr7:3340666-3340675
6	CTCF	chr7:3340540-3340690	BJ	skin:	n/a	n/a
7	CTCF	chr7:3340540-3340690	HPF	lung:	n/a	n/a
8	RUNX3	chr7:3340464-3340779	GM12878	blood:	n/a	n/a
9	USF1	chr7:3340548-3340770	SK-N-SH_RA	brain:	n/a	n/a
10	MAZ	chr7:3340423-3340911	GM12878	blood:	n/a	chr7:3340556-3340566
11	RAD21	chr7:3340160-3340979	MCF-7	breast:	n/a	n/a
12	CTCF	chr7:3340520-3340670	HEK293	kidney:	n/a	n/a
13	MAX	chr7:3340236-3341061	HCT-116	colon:	n/a	chr7:3340556-3340566
14	HCFC1	chr7:3340586-3340786	K562	blood:	n/a	n/a
15	POLR2A	chr7:3340452-3340913	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr7:3340358-3340781	MCF-7	breast:	n/a	chr7:3340483-3340496
17	CTCF	chr7:3340445-3340787	GM13977	blood:	n/a	chr7:3340483-3340496
18	MAX	chr7:3340519-3340789	Hela-S3	cervix:	n/a	chr7:3340556-3340566
19	CTCF	chr7:3339276-3341235	SK-N-SH	brain:	n/a	chr7:3339295-3339303 chr7:3340483-3340496 chr7:3339382-3339390
20	POLR2A	chr7:3340593-3340771	ProgFib	skin:	n/a	n/a
21	CTCF	chr7:3340520-3340670	HCM	heart:	n/a	n/a
22	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
23	EP300	chr7:3340578-3340765	HepG2	liver:	n/a	chr7:3340748-3340757 chr7:3340695-3340704 chr7:3340638-3340647 chr7:3340735-3340751
24	RAD21	chr7:3340488-3340794	GM12878	blood:	n/a	n/a
25	CTCF	chr7:3340520-3340670	HRPEpiC	eye:	n/a	n/a
26	CTCF	chr7:3340433-3340874	A549	lung:	n/a	chr7:3340483-3340496
27	CTCF	chr7:3340464-3340760	Fibrobl	skin:	n/a	chr7:3340483-3340496
28	CTCF	chr7:3340520-3340670	HCFaa	heart:	n/a	n/a
29	MAX	chr7:3340278-3341002	H1-hESC	embryonic stem cell:	n/a	chr7:3340556-3340566
30	ELF1	chr7:3340543-3340734	K562	blood:	n/a	n/a
31	TCF12	chr7:3340537-3340722	GM12878	blood:	n/a	n/a
32	RAD21	chr7:3340369-3340901	HCT-116	colon:	n/a	n/a
33	RAD21	chr7:3340445-3340896	HepG2	liver:	n/a	n/a
34	CTCF	chr7:3340470-3340763	MCF-7	breast:	n/a	chr7:3340483-3340496
35	CHD2	chr7:3340488-3340695	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr7:3340520-3340670	Hela-S3	cervix:	n/a	n/a
37	RAD21	chr7:3340288-3340949	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr7:3340560-3340710	GM12869	blood:	n/a	n/a
39	POLR2A	chr7:3340214-3341121	MCF-7	breast:	n/a	n/a
40	ARID3A	chr7:3340510-3340769	HepG2	liver:	n/a	n/a
41	YY1	chr7:3340284-3340751	GM12891	blood:	n/a	chr7:3340664-3340678 chr7:3340464-3340475 chr7:3340661-3340675 chr7:3340666-3340675
42	CTCF	chr7:3340520-3340670	WERI-Rb-1	eye:	n/a	n/a
43	MAX	chr7:3340431-3340992	K562	blood:	n/a	chr7:3340556-3340566
44	RAD21	chr7:3340369-3340948	SK-N-SH_RA	brain:	n/a	n/a
45	RAD21	chr7:3340392-3340764	A549	lung:	n/a	n/a
46	CTCF	chr7:3340600-3340750	WI-38	lung:	n/a	n/a
47	CTCF	chr7:3340540-3340690	GM12872	blood:	n/a	n/a
48	CTCF	chr7:3340560-3340710	GM12864	blood:	n/a	n/a
49	E2F6	chr7:3340434-3340956	K562	blood:	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
50	YY1	chr7:3340300-3340931	HepG2	liver:	n/a	chr7:3340750-3340759 chr7:3340664-3340678 chr7:3340464-3340475 chr7:3340661-3340675 chr7:3340745-3340759 chr7:3340666-3340675

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: 26 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:26 , 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	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	esv3421283	chr7:3340376-3342024	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv605890	chr7:3340396-3341488	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	esv1833976	chr7:3340396-3341589	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv605891	chr7:3340500-3341589	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3339600-3342600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr7:3339800-3341600	Active TSS	Fetal Brain Female	brain
3	chr7:3339800-3342200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:3339800-3342200	Active TSS	HSMMtube	muscle
5	chr7:3340000-3341600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:3340000-3341600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:3340000-3342200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:3340000-3342200	Active TSS	HepG2	liver
9	chr7:3340000-3342200	Active TSS	HSMM	muscle
10	chr7:3340000-3342400	Active TSS	Right Atrium	heart
11	chr7:3340000-3342600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr7:3340000-3342600	Active TSS	Rectal Smooth Muscle	rectum
13	chr7:3340000-3343400	Active TSS	Aorta	Aorta
14	chr7:3340200-3341200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:3340200-3341400	Active TSS	Psoas Muscle	Psoas
16	chr7:3340200-3341400	Active TSS	Right Ventricle	heart
17	chr7:3340200-3341600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr7:3340200-3341600	Active TSS	Stomach Smooth Muscle	stomach
19	chr7:3340200-3341600	Active TSS	A549	lung
20	chr7:3340200-3341800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:3340200-3342000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:3340200-3342000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:3340200-3342400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:3340200-3342400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr7:3340200-3342400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:3340200-3342400	Active TSS	Ovary	ovary
27	chr7:3340200-3342400	Active TSS	Pancreas	Pancrea
28	chr7:3340200-3342800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:3340200-3343000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr7:3340200-3343200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:3340400-3340800	Bivalent/Poised TSS	Fetal Stomach	stomach
32	chr7:3340400-3340800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
33	chr7:3340400-3340800	Bivalent/Poised TSS	Osteobl	bone
34	chr7:3340400-3341200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:3340400-3341400	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr7:3340400-3341400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:3340400-3341400	Active TSS	HUVEC	blood vessel
38	chr7:3340400-3341600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:3340400-3341600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr7:3340400-3341600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr7:3340400-3341600	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr7:3340400-3341600	Active TSS	Duodenum Mucosa	Duodenum
43	chr7:3340400-3341600	Weak transcription	Fetal Heart	heart
44	chr7:3340400-3341600	Active TSS	Fetal Muscle Leg	muscle
45	chr7:3340400-3341600	Active TSS	NHLF	lung
46	chr7:3340400-3341800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:3340400-3342000	Active TSS	Gastric	stomach
48	chr7:3340400-3342200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr7:3340400-3342200	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr7:3340400-3342200	Active TSS	Left Ventricle	heart

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