Variant report

Variant	rs17825523
Chromosome Location	chr3:56591904-56591905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:119)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:119 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:56590599-56591968	HepG2	liver:	n/a	n/a
2	MAZ	chr3:56590848-56592052	GM12878	blood:	n/a	n/a
3	GTF2F1	chr3:56590904-56592042	Hela-S3	cervix:	n/a	n/a
4	FOS	chr3:56591785-56591943	MCF10A-Er-Src	breast:	n/a	n/a
5	KAP1	chr3:56591012-56592291	HEK293	kidney:	n/a	n/a
6	E2F4	chr3:56590978-56592027	MCF10A-Er-Src	breast:	n/a	n/a
7	CHD1	chr3:56590763-56591987	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr3:56591573-56591972	ECC-1	luminal epithelium:	n/a	n/a
9	WRNIP1	chr3:56591313-56592350	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:56590779-56591935	GM12878	blood:	n/a	n/a
11	MYC	chr3:56590883-56592018	K562	blood:	n/a	n/a
12	CTCF	chr3:56591554-56591931	HepG2	liver:	n/a	n/a
13	YY1	chr3:56591611-56591905	HCT-116	colon:	n/a	n/a
14	CTCF	chr3:56591629-56591910	K562	blood:	n/a	n/a
15	FOS	chr3:56591801-56591999	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr3:56591066-56592085	GM12878	blood:	n/a	n/a
17	SMC3	chr3:56590931-56591921	Hela-S3	cervix:	n/a	chr3:56591610-56591620
18	TBP	chr3:56590927-56592299	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr3:56591618-56591943	SK-N-SH_RA	brain:	n/a	n/a
20	CHD2	chr3:56590971-56591918	K562	blood:	n/a	n/a
21	MXI1	chr3:56590612-56592100	Hela-S3	cervix:	n/a	n/a
22	MAX	chr3:56590830-56591956	ECC-1	luminal epithelium:	n/a	n/a
23	MYC	chr3:56590487-56591972	K562	blood:	n/a	n/a
24	POLR2A	chr3:56590925-56592736	K562	blood:	n/a	n/a
25	HEY1	chr3:56590924-56592246	K562	blood:	n/a	chr3:56591093-56591108
26	RUNX3	chr3:56591547-56592109	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:56590356-56592659	MCF10A-Er-Src	breast:	n/a	n/a
28	CTCF	chr3:56591649-56591938	A549	lung:	n/a	n/a
29	POLR2A	chr3:56590499-56592047	K562	blood:	n/a	n/a
30	MAX	chr3:56590898-56591984	NB4	blood:	n/a	n/a
31	POLR2A	chr3:56590805-56591927	HL-60	blood:	n/a	n/a
32	MYC	chr3:56591046-56591988	MCF10A-Er-Src	breast:	n/a	n/a
33	CHD2	chr3:56590702-56592462	GM12878	blood:	n/a	n/a
34	CTCF	chr3:56591085-56592044	K562	blood:	n/a	n/a
35	MYC	chr3:56590964-56591937	K562	blood:	n/a	n/a
36	CTCF	chr3:56591407-56592324	A549	lung:	n/a	n/a
37	TAL1	chr3:56590768-56591941	K562	blood:	n/a	n/a
38	MYC	chr3:56591395-56592054	A549	lung:	n/a	n/a
39	MAX	chr3:56590907-56591969	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr3:56590802-56591937	Hela-S3	cervix:	n/a	n/a
41	MAX	chr3:56590905-56591958	H1-hESC	embryonic stem cell:	n/a	n/a
42	STAT1	chr3:56590945-56591932	GM12878	blood:	n/a	chr3:56591405-56591417 chr3:56591549-56591561
43	MAX	chr3:56590720-56592093	HCT-116	colon:	n/a	n/a
44	RCOR1	chr3:56590955-56592132	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:56590569-56592147	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr3:56591522-56591963	K562	blood:	n/a	n/a
47	POLR2A	chr3:56590698-56592429	PBDE	blood:	n/a	n/a
48	MAX	chr3:56590869-56591925	K562	blood:	n/a	n/a
49	ZNF143	chr3:56591003-56592444	GM12878	blood:	n/a	chr3:56591394-56591404
50	ZNF143	chr3:56591605-56591931	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
2	chr3:56588808..56592620-chr3:56662133..56663692,3	K562	blood:
3	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
4	chr3:56589716..56592620-chr3:56662133..56663652,2	K562	blood:

No data

Variant related genes	Relation type
CCDC66	TF binding region
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11130526	0.86[CEU][hapmap]
rs17235662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3417076	chr3:56590062-56591960	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17825523	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56590000-56592000	Active TSS	NHDF-Ad	bronchial
2	chr3:56590200-56592000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:56590200-56592000	Active TSS	Duodenum Mucosa	Duodenum
4	chr3:56590200-56592000	Active TSS	Fetal Heart	heart
5	chr3:56590200-56592000	Active TSS	Fetal Kidney	kidney
6	chr3:56590200-56592600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:56590200-56592600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:56590200-56592600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:56590200-56592600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:56590400-56592000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:56590400-56592000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:56590400-56592000	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr3:56590400-56592000	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:56590400-56592000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:56590400-56592000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr3:56590400-56592000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:56590400-56592000	Active TSS	Brain Anterior Caudate	brain
18	chr3:56590400-56592000	Active TSS	Brain Cingulate Gyrus	brain
19	chr3:56590400-56592000	Active TSS	Brain Hippocampus Middle	brain
20	chr3:56590400-56592000	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr3:56590400-56592000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr3:56590400-56592000	Active TSS	Fetal Muscle Leg	muscle
23	chr3:56590400-56592000	Active TSS	Placenta Amnion	Placenta Amnion
24	chr3:56590400-56592000	Active TSS	Psoas Muscle	Psoas
25	chr3:56590400-56592000	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:56590400-56592000	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:56590400-56592000	Active TSS	Hela-S3	cervix
28	chr3:56590400-56592000	Active TSS	NH-A	brain
29	chr3:56590400-56592000	Active TSS	Osteobl	bone
30	chr3:56590400-56592200	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr3:56590400-56592200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:56590400-56592200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr3:56590400-56592200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:56590400-56592200	Active TSS	Fetal Intestine Large	intestine
35	chr3:56590400-56592200	Active TSS	Fetal Intestine Small	intestine
36	chr3:56590400-56592200	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr3:56590400-56592200	Active TSS	Stomach Smooth Muscle	stomach
38	chr3:56590400-56592200	Active TSS	NHEK	skin
39	chr3:56590400-56592400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr3:56590400-56592400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:56590400-56592400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:56590400-56592400	Active TSS	Fetal Muscle Trunk	muscle
43	chr3:56590400-56592400	Active TSS	Right Ventricle	heart
44	chr3:56590400-56592600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr3:56590400-56592600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:56590400-56592600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:56590400-56592600	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr3:56590400-56592600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr3:56590400-56592600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:56590400-56592600	Active TSS	Breast Myoepithelial Primary Cells	Breast

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