Variant report

Variant	rs17235662
Chromosome Location	chr3:56592005-56592006
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr3:56590848-56592052	GM12878	blood:	n/a	n/a
2	GTF2F1	chr3:56590904-56592042	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr3:56592000-56592150	Caco-2	colon:	n/a	n/a
4	KAP1	chr3:56591012-56592291	HEK293	kidney:	n/a	n/a
5	E2F4	chr3:56590978-56592027	MCF10A-Er-Src	breast:	n/a	n/a
6	WRNIP1	chr3:56591313-56592350	GM12878	blood:	n/a	n/a
7	MYC	chr3:56590883-56592018	K562	blood:	n/a	n/a
8	CTCF	chr3:56591066-56592085	GM12878	blood:	n/a	n/a
9	TBP	chr3:56590927-56592299	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr3:56590612-56592100	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:56590925-56592736	K562	blood:	n/a	n/a
12	HEY1	chr3:56590924-56592246	K562	blood:	n/a	chr3:56591093-56591108
13	RUNX3	chr3:56591547-56592109	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:56590356-56592659	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:56590499-56592047	K562	blood:	n/a	n/a
16	CHD2	chr3:56590702-56592462	GM12878	blood:	n/a	n/a
17	CTCF	chr3:56591085-56592044	K562	blood:	n/a	n/a
18	CTCF	chr3:56592000-56592150	SAEC	small airway:	n/a	n/a
19	CTCF	chr3:56591407-56592324	A549	lung:	n/a	n/a
20	MYC	chr3:56591395-56592054	A549	lung:	n/a	n/a
21	MAX	chr3:56590720-56592093	HCT-116	colon:	n/a	n/a
22	RCOR1	chr3:56590955-56592132	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:56590569-56592147	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:56590698-56592429	PBDE	blood:	n/a	n/a
25	ZNF143	chr3:56591003-56592444	GM12878	blood:	n/a	chr3:56591394-56591404
26	CEBPB	chr3:56590685-56592055	Hela-S3	cervix:	n/a	chr3:56591677-56591694
27	E2F6	chr3:56590909-56592013	A549	lung:	n/a	n/a
28	MAZ	chr3:56590709-56592061	IMR90	lung:	n/a	n/a
29	EBF1	chr3:56591634-56592472	GM12878	blood:	n/a	n/a
30	CTCF	chr3:56591220-56592123	IMR90	lung:	n/a	n/a
31	SIN3A	chr3:56590484-56592278	H1-hESC	embryonic stem cell:	n/a	n/a
32	FOS	chr3:56591923-56592162	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr3:56590770-56592215	GM12891	blood:	n/a	n/a
34	TBP	chr3:56590528-56592139	K562	blood:	n/a	n/a
35	ZNF263	chr3:56590985-56592151	HEK293-T-REx	kidney:	n/a	chr3:56591544-56591565
36	KAP1	chr3:56591228-56592016	U2OS	brain:	n/a	n/a
37	MAX	chr3:56590909-56592017	A549	lung:	n/a	n/a
38	MYC	chr3:56591072-56592007	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr3:56590590-56592032	K562	blood:	n/a	n/a
40	MAX	chr3:56590829-56592076	HCT-116	colon:	n/a	n/a
41	POLR2A	chr3:56590826-56592015	GM18505	blood:	n/a	n/a
42	MXI1	chr3:56590934-56592520	IMR90	lung:	n/a	n/a
43	MAFK	chr3:56591073-56592188	Hela-S3	cervix:	n/a	n/a
44	CHD1	chr3:56590974-56592404	GM12878	blood:	n/a	n/a
45	ARID3A	chr3:56591601-56592288	K562	blood:	n/a	n/a
46	HCFC1	chr3:56590644-56592693	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr3:56590850-56592324	Hela-S3	cervix:	n/a	n/a
48	EP300	chr3:56590970-56592178	GM12878	blood:	n/a	chr3:56591111-56591127
49	ARID3A	chr3:56591600-56592272	HepG2	liver:	n/a	n/a
50	PML	chr3:56590712-56592079	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:56588808..56592620-chr3:56662133..56663692,3	K562	blood:
2	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
3	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: 6 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11130526	0.88[CEU][hapmap]
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]
rs17825523	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:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17235662	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	chr3:56590200-56592600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:56590200-56592600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:56590200-56592600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr3:56590200-56592600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:56590400-56592200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:56590400-56592200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:56590400-56592200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr3:56590400-56592200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:56590400-56592200	Active TSS	Fetal Intestine Large	intestine
10	chr3:56590400-56592200	Active TSS	Fetal Intestine Small	intestine
11	chr3:56590400-56592200	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr3:56590400-56592200	Active TSS	Stomach Smooth Muscle	stomach
13	chr3:56590400-56592200	Active TSS	NHEK	skin
14	chr3:56590400-56592400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr3:56590400-56592400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:56590400-56592400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:56590400-56592400	Active TSS	Fetal Muscle Trunk	muscle
18	chr3:56590400-56592400	Active TSS	Right Ventricle	heart
19	chr3:56590400-56592600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr3:56590400-56592600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:56590400-56592600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:56590400-56592600	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:56590400-56592600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:56590400-56592600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:56590400-56592600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr3:56590400-56592600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:56590400-56592600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:56590400-56592600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:56590400-56592600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:56590400-56592600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:56590400-56592600	Active TSS	Right Atrium	heart
32	chr3:56590400-56592600	Active TSS	Thymus	Thymus
33	chr3:56590400-56592600	Active TSS	NHLF	lung
34	chr3:56590400-56592800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:56590400-56592800	Active TSS	A549	lung
36	chr3:56590400-56593000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr3:56590400-56593000	Active TSS	HMEC	breast
38	chr3:56590400-56593000	Active TSS	K562	blood
39	chr3:56590400-56593400	Active TSS	GM12878-XiMat	blood
40	chr3:56590600-56592200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:56590600-56592200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:56590600-56592200	Active TSS	HSMM	muscle
43	chr3:56590600-56592400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:56590600-56592400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:56590600-56592400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:56590600-56592400	Active TSS	Placenta	Placenta
47	chr3:56590600-56592400	Active TSS	Ovary	ovary
48	chr3:56590600-56592400	Active TSS	Stomach Mucosa	stomach
49	chr3:56590600-56592600	Active TSS	Colonic Mucosa	Colon
50	chr3:56590800-56592400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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