Variant report

Variant	rs13099722
Chromosome Location	chr3:56592234-56592235
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	KAP1	chr3:56591012-56592291	HEK293	kidney:	n/a	n/a
2	WRNIP1	chr3:56591313-56592350	GM12878	blood:	n/a	n/a
3	TBP	chr3:56590927-56592299	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:56590925-56592736	K562	blood:	n/a	n/a
5	HEY1	chr3:56590924-56592246	K562	blood:	n/a	chr3:56591093-56591108
6	YY1	chr3:56592075-56592382	SK-N-SH_RA	brain:	n/a	chr3:56592254-56592276 chr3:56592254-56592264
7	POLR2A	chr3:56590356-56592659	MCF10A-Er-Src	breast:	n/a	n/a
8	YY1	chr3:56592119-56592365	K562	blood:	n/a	chr3:56592254-56592276 chr3:56592254-56592264
9	CHD2	chr3:56590702-56592462	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:56592151-56592318	K562	blood:	n/a	n/a
11	CTCF	chr3:56591407-56592324	A549	lung:	n/a	n/a
12	POLR2A	chr3:56590698-56592429	PBDE	blood:	n/a	n/a
13	ZNF143	chr3:56591003-56592444	GM12878	blood:	n/a	chr3:56591394-56591404
14	EBF1	chr3:56591634-56592472	GM12878	blood:	n/a	n/a
15	SIN3A	chr3:56590484-56592278	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:56592208-56592326	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr3:56592140-56592290	HEEpiC	esophagus:	n/a	n/a
18	MXI1	chr3:56590934-56592520	IMR90	lung:	n/a	n/a
19	CHD1	chr3:56590974-56592404	GM12878	blood:	n/a	n/a
20	ARID3A	chr3:56591601-56592288	K562	blood:	n/a	n/a
21	HCFC1	chr3:56590644-56592693	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:56590850-56592324	Hela-S3	cervix:	n/a	n/a
23	ARID3A	chr3:56591600-56592272	HepG2	liver:	n/a	n/a
24	TBP	chr3:56590941-56592569	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:56590174-56592533	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:56590840-56592479	HepG2	liver:	n/a	n/a
27	CTCF	chr3:56590943-56592441	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr3:56592140-56592290	HPF	lung:	n/a	n/a

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:

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

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13060656	0.82[CEU][hapmap]
rs13068670	0.82[CEU][hapmap]
rs13074639	0.82[CEU][hapmap]
rs13086565	0.82[CEU][hapmap]
rs13093466	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34558590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35995233	1.00[AFR][1000 genomes]
rs6807338	0.82[CEU][hapmap]
rs71309971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][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

No data

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	chr3:56590400-56592400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:56590400-56592400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:56590400-56592400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:56590400-56592400	Active TSS	Fetal Muscle Trunk	muscle
9	chr3:56590400-56592400	Active TSS	Right Ventricle	heart
10	chr3:56590400-56592600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr3:56590400-56592600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:56590400-56592600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:56590400-56592600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:56590400-56592600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:56590400-56592600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:56590400-56592600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr3:56590400-56592600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:56590400-56592600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:56590400-56592600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:56590400-56592600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:56590400-56592600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:56590400-56592600	Active TSS	Right Atrium	heart
23	chr3:56590400-56592600	Active TSS	Thymus	Thymus
24	chr3:56590400-56592600	Active TSS	NHLF	lung
25	chr3:56590400-56592800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:56590400-56592800	Active TSS	A549	lung
27	chr3:56590400-56593000	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:56590400-56593000	Active TSS	HMEC	breast
29	chr3:56590400-56593000	Active TSS	K562	blood
30	chr3:56590400-56593400	Active TSS	GM12878-XiMat	blood
31	chr3:56590600-56592400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:56590600-56592400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:56590600-56592400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:56590600-56592400	Active TSS	Placenta	Placenta
35	chr3:56590600-56592400	Active TSS	Ovary	ovary
36	chr3:56590600-56592400	Active TSS	Stomach Mucosa	stomach
37	chr3:56590600-56592600	Active TSS	Colonic Mucosa	Colon
38	chr3:56590800-56592400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:56590800-56592400	Active TSS	Esophagus	oesophagus
40	chr3:56590800-56592400	Active TSS	Gastric	stomach
41	chr3:56590800-56592400	Active TSS	Left Ventricle	heart
42	chr3:56590800-56592400	Active TSS	Lung	lung
43	chr3:56590800-56592400	Active TSS	Pancreas	Pancrea
44	chr3:56590800-56592600	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr3:56591000-56592400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:56591200-56592400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:56591200-56592600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr3:56591200-56592800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:56591400-56592400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr3:56591400-56592600	Active TSS	Aorta	Aorta

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