Variant report

Variant	rs563756584
Chromosome Location	chr2:56410678-56410679
allele	C/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	POLR2A	chr2:56408936-56411912	K562	blood:	n/a	n/a
2	CTCF	chr2:56410646-56411048	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr2:56410650-56410989	A549	lung:	n/a	n/a
4	CTCF	chr2:56410650-56410974	A549	lung:	n/a	n/a
5	POLR2A	chr2:56410670-56411469	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr2:56410405-56411276	A549	lung:	n/a	n/a
7	RUNX3	chr2:56410647-56411040	GM12878	blood:	n/a	n/a
8	SIN3AK20	chr2:56410584-56411500	MCF-7	breast:	n/a	n/a
9	RAD21	chr2:56410567-56411274	HCT-116	colon:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
10	CTCF	chr2:56410619-56411036	HepG2	liver:	n/a	n/a
11	CTCF	chr2:56410569-56411145	MCF-7	breast:	n/a	n/a
12	RAD21	chr2:56410617-56411211	MCF-7	breast:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
13	POU2F2	chr2:56410634-56410933	GM12878	blood:	n/a	chr2:56410708-56410722
14	RAD21	chr2:56410608-56411082	H1-hESC	embryonic stem cell:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881
15	TAF1	chr2:56410673-56412158	SK-N-SH	brain:	n/a	n/a
16	REST	chr2:56410616-56411804	H1-neurons	neurons:	n/a	chr2:56411082-56411092 chr2:56411303-56411313 chr2:56410985-56411003 chr2:56411429-56411439 chr2:56411313-56411326 chr2:56411670-56411683 chr2:56411737-56411750
17	SMC3	chr2:56410656-56411141	Hela-S3	cervix:	n/a	chr2:56410966-56410976 chr2:56410867-56410881
18	RAD21	chr2:56410582-56411217	H1-hESC	embryonic stem cell:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
19	RAD21	chr2:56410592-56411186	HepG2	liver:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
20	CTCF	chr2:56410652-56411068	K562	blood:	n/a	n/a
21	RAD21	chr2:56410672-56411062	HepG2	liver:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881
22	RAD21	chr2:56410615-56411439	SK-N-SH	brain:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
23	CTCF	chr2:56410646-56411162	GM12878	blood:	n/a	n/a
24	NFIC	chr2:56410678-56410983	HepG2	liver:	n/a	n/a
25	MAX	chr2:56410628-56411241	SK-N-SH	brain:	n/a	chr2:56411109-56411119
26	RAD21	chr2:56410660-56411076	GM12878	blood:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881
27	RAD21	chr2:56410665-56411360	H1-hESC	embryonic stem cell:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
28	POLR2A	chr2:56410644-56412125	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr2:56410666-56411249	MCF-7	breast:	n/a	n/a
30	SMC3	chr2:56410649-56411061	GM12878	blood:	n/a	chr2:56410966-56410976 chr2:56410867-56410881
31	PBX3	chr2:56410623-56411329	SK-N-SH	brain:	n/a	n/a
32	SIN3AK20	chr2:56410618-56411440	SK-N-SH	brain:	n/a	n/a
33	RAD21	chr2:56410608-56411117	A549	lung:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
34	MAX	chr2:56410659-56411323	MCF-7	breast:	n/a	chr2:56411109-56411119
35	POLR2A	chr2:56410625-56411483	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr2:56410652-56411275	SK-N-SH	brain:	n/a	chr2:56411109-56411119
37	BHLHE40	chr2:56410676-56411058	K562	blood:	n/a	chr2:56410938-56410954
38	RAD21	chr2:56410664-56411288	SK-N-SH_RA	brain:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
39	RAD21	chr2:56410645-56411248	ECC-1	luminal epithelium:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
40	MAZ	chr2:56410617-56411517	IMR90	lung:	n/a	chr2:56411109-56411119
41	CTCF	chr2:56410591-56411226	HCT-116	colon:	n/a	n/a
42	RAD21	chr2:56410618-56411258	HCT-116	colon:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
43	RAD21	chr2:56410597-56411244	A549	lung:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
44	TCF12	chr2:56410636-56411099	A549	lung:	n/a	n/a
45	CTCF	chr2:56410581-56411188	HCT-116	colon:	n/a	n/a
46	SMC3	chr2:56410455-56411589	SK-N-SH	brain:	n/a	chr2:56410966-56410976 chr2:56410867-56410881
47	FOXM1	chr2:56410672-56411146	GM12878	blood:	n/a	n/a
48	HDAC2	chr2:56410609-56411406	MCF-7	breast:	n/a	n/a
49	RAD21	chr2:56410676-56411079	Hela-S3	cervix:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881
50	RAD21	chr2:56410609-56410999	ECC-1	luminal epithelium:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:56410676-56410726	HCPEpiC	choroid plexus:	n/a
2	chr2:56410676-56410726	GM12878	blood:	n/a
3	chr2:56410676-56410726	HCT-116	colon:	n/a
4	chr2:56410676-56410726	SKMC	muscle:	n/a
5	chr2:56410676-56410726	U87	brain:	n/a
6	chr2:56410676-56410726	PFSK-1	brain:	n/a
7	chr2:56410676-56410726	HEK293	kidney:	embryo
8	chr2:56410676-56410726	GM12891	blood:	n/a
9	chr2:56410676-56410726	HRPEpiC	eye:	n/a
10	chr2:56410676-56410726	IMR90	lung:	fetal
11	chr2:56410676-56410726	Hepatocyte	liver:	n/a
12	chr2:56410676-56410726	ovcar-3	ovarian:	n/a
13	chr2:56410676-56410726	HMEC	breast:	n/a
14	chr2:56410676-56410726	SAEC	small airway:	n/a
15	chr2:56410676-56410726	A549	lung:	n/a
16	chr2:56410676-56410726	BE2_C	brain:	n/a
17	chr2:56410676-56410726	BJ	skin:	n/a
18	chr2:56410676-56410726	HRE	kidney:	n/a
19	chr2:56410676-56410726	HEEpiC	esophagus:	n/a
20	chr2:56410676-56410726	HepG2	liver:	n/a
21	chr2:56410676-56410726	HUVEC	blood vessel:	n/a
22	chr2:56410676-56410726	NT2-D1	testis:	n/a
23	chr2:56410676-56410726	LNCaP	prostate:	n/a
24	chr2:56410676-56410726	RPTEC	kidney:	n/a
25	chr2:56410676-56410726	PANC-1	pancreas:	n/a
26	chr2:56410676-56410726	AG04450	lung:	fetal
27	chr2:56410676-56410726	MCF-7	breast:	n/a
28	chr2:56410676-56410726	AG04449	skin:	fetal
29	chr2:56410676-56410726	AG09319	gingival:	n/a
30	chr2:56410676-56410726	HAEpiC	amniotic membrane:	n/a
31	chr2:56410676-56410726	NHDF-neo	bronchial:	n/a
32	chr2:56410676-56410726	AG10803	skin:	n/a
33	chr2:56410676-56410726	HCF	heart:	n/a
34	chr2:56410676-56410726	CMK	blood:	n/a
35	chr2:56410676-56410726	Jurkat	blood:	n/a
36	chr2:56410676-56410726	NH-A	brain:	n/a
37	chr2:56410676-56410726	T-47D	breast:	n/a
38	chr2:56410676-56410726	HIPEpiC	eye:	n/a
39	chr2:56410676-56410726	GM12892	blood:	n/a
40	chr2:56410676-56410726	NB4	blood:	n/a
41	chr2:56410676-56410726	K562	blood:	n/a
42	chr2:56410676-56410726	GM19239	blood:	n/a
43	chr2:56410676-56410726	Hela-S3	cervix:	n/a
44	chr2:56410676-56410726	HNPCEpiC	eye:	n/a
45	chr2:56410676-56410726	MCF10A-Er-Src	breast:	n/a
46	chr2:56410676-56410726	HL-60	blood:	n/a
47	chr2:56410676-56410726	SK-N-SH	brain:	n/a
48	chr2:56410676-56410726	Caco-2	colon:	n/a
49	chr2:56410676-56410726	SK-N-SH_RA	brain:	n/a
50	chr2:56410676-56410726	HCM	heart:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFEMP1-3	chr2:56410502-56410809	NONHSAT070825

Variant related genes	Relation type
CCDC85A	TF binding region
CCDC85A	CpG island

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription 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
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2762648	chr2:56386656-56422448	Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3411625	chr2:56409873-56412421	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3442902	chr2:56410148-56412896	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3330480	chr2:56410673-56413221	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56409000-56410800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:56409200-56411000	Enhancers	Placenta	Placenta
3	chr2:56409400-56411200	Weak transcription	Fetal Heart	heart
4	chr2:56409800-56411000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:56410000-56410800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:56410000-56410800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:56410000-56410800	Enhancers	Primary hematopoietic stem cells	blood
8	chr2:56410000-56411000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr2:56410200-56410800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
10	chr2:56410200-56411000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
11	chr2:56410400-56412800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:56410600-56410800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:56410600-56410800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr2:56410600-56410800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr2:56410600-56410800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:56410600-56410800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:56410600-56410800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
18	chr2:56410600-56410800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:56410600-56410800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:56410600-56410800	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr2:56410600-56410800	Bivalent Enhancer	Liver	Liver
22	chr2:56410600-56410800	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr2:56410600-56410800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr2:56410600-56410800	Enhancers	Brain Substantia Nigra	brain
25	chr2:56410600-56410800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
26	chr2:56410600-56410800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr2:56410600-56410800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
28	chr2:56410600-56410800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:56410600-56410800	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr2:56410600-56410800	Enhancers	Left Ventricle	heart
31	chr2:56410600-56410800	Enhancers	Ovary	ovary
32	chr2:56410600-56410800	Enhancers	Pancreas	Pancrea
33	chr2:56410600-56410800	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:56410600-56410800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr2:56410600-56410800	Bivalent Enhancer	A549	lung
36	chr2:56410600-56410800	Flanking Active TSS	Hela-S3	cervix
37	chr2:56410600-56410800	Flanking Active TSS	HUVEC	blood vessel
38	chr2:56410600-56411000	Bivalent Enhancer	Fetal Thymus	thymus
39	chr2:56410600-56411200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
40	chr2:56410600-56411200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:56410600-56411200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:56410600-56411200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:56410600-56411200	Active TSS	Right Ventricle	heart
44	chr2:56410600-56411400	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr2:56410600-56411600	Active TSS	Lung	lung
46	chr2:56410600-56411600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
47	chr2:56410600-56411800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr2:56410600-56411800	Enhancers	Fetal Brain Male	brain
49	chr2:56410600-56411800	Active TSS	Fetal Brain Female	brain
50	chr2:56410600-56411800	Bivalent/Poised TSS	Fetal Stomach	stomach

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