Variant report

Variant	rs1565378
Chromosome Location	chr3:56717556-56717557
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	TEAD4	chr3:56717176-56717647	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:56716248-56717684	MCF-7	breast:	n/a	n/a
3	CHD2	chr3:56716259-56717657	GM12878	blood:	n/a	n/a
4	PBX3	chr3:56716349-56717649	SK-N-SH	brain:	n/a	n/a
5	MAZ	chr3:56716161-56717571	HepG2	liver:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
6	POLR2A	chr3:56716232-56717582	HL-60	blood:	n/a	n/a
7	MAX	chr3:56716035-56717842	HepG2	liver:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
8	TCF12	chr3:56717134-56717705	ECC-1	luminal epithelium:	n/a	n/a
9	TBP	chr3:56716263-56717591	K562	blood:	n/a	n/a
10	POU2F2	chr3:56716348-56717567	GM12891	blood:	n/a	chr3:56716636-56716658 chr3:56717304-56717316
11	POLR2A	chr3:56716161-56717724	GM19099	blood:	n/a	n/a
12	TAL1	chr3:56716383-56717821	K562	blood:	n/a	n/a
13	MXI1	chr3:56716155-56717683	GM12878	blood:	n/a	n/a
14	MAX	chr3:56716250-56717788	H1-hESC	embryonic stem cell:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
15	CBX3	chr3:56716207-56717929	HCT-116	colon:	n/a	n/a
16	RCOR1	chr3:56716367-56717805	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:56716223-56717594	HepG2	liver:	n/a	n/a
18	MAZ	chr3:56716250-56717657	K562	blood:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
19	GATA1	chr3:56716189-56718152	PBDE	blood:	n/a	chr3:56717810-56717821
20	MAX	chr3:56716100-56717821	SK-N-SH	brain:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
21	STAT1	chr3:56717206-56717606	GM12878	blood:	n/a	chr3:56717262-56717274 chr3:56717298-56717310
22	EGR1	chr3:56717132-56717558	GM12878	blood:	n/a	chr3:56717304-56717314 chr3:56717303-56717317 chr3:56717302-56717315 chr3:56717138-56717151 chr3:56717307-56717317 chr3:56717302-56717315 chr3:56717301-56717316
23	JUND	chr3:56716327-56717607	K562	blood:	n/a	chr3:56717334-56717343
24	CTCF	chr3:56717369-56717565	GM12878	blood:	n/a	chr3:56717378-56717391
25	MAX	chr3:56716356-56717722	HUVEC	blood vessel:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
26	MYC	chr3:56716246-56717640	K562	blood:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
27	POLR2A	chr3:56716220-56717670	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr3:56715800-56717661	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:56716156-56717731	Raji	blood:	n/a	n/a
30	CBX3	chr3:56717044-56718024	K562	blood:	n/a	chr3:56717939-56717950
31	CHD2	chr3:56716466-56717652	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:56716216-56717556	HCT-116	colon:	n/a	n/a
33	POLR2A	chr3:56716948-56717673	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr3:56716303-56717610	A549	lung:	n/a	n/a
35	POLR2A	chr3:56716057-56717627	Hela-S3	cervix:	n/a	n/a
36	ELF1	chr3:56717205-56717575	A549	lung:	n/a	n/a
37	HMGN3	chr3:56716391-56717642	K562	blood:	n/a	n/a
38	HEY1	chr3:56716786-56717557	K562	blood:	n/a	chr3:56717313-56717328 chr3:56717344-56717359
39	EP300	chr3:56717399-56717651	K562	blood:	n/a	chr3:56717514-56717530 chr3:56717453-56717469
40	CEBPB	chr3:56717406-56717603	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr3:56716286-56717648	K562	blood:	n/a	chr3:56717304-56717318 chr3:56716655-56716665 chr3:56717307-56717316 chr3:56717098-56717107 chr3:56716908-56716920 chr3:56716581-56716595
42	E2F6	chr3:56716268-56718072	A549	lung:	n/a	chr3:56717409-56717419 chr3:56717410-56717418 chr3:56717098-56717107 chr3:56717408-56717419 chr3:56717562-56717571 chr3:56717410-56717418 chr3:56717307-56717316 chr3:56717411-56717418 chr3:56717410-56717418
43	TCF7L2	chr3:56717403-56718599	HEK293	kidney:	n/a	n/a
44	POLR2A	chr3:56716182-56717592	GM12878	blood:	n/a	n/a
45	MXI1	chr3:56715930-56717675	IMR90	lung:	n/a	n/a
46	MAX	chr3:56716139-56717768	NB4	blood:	n/a	chr3:56716408-56716418 chr3:56717305-56717315
47	NRF1	chr3:56717143-56717563	GM12878	blood:	n/a	chr3:56717352-56717363 chr3:56717354-56717363 chr3:56717307-56717316
48	NFYA	chr3:56717063-56717770	Hela-S3	cervix:	n/a	chr3:56717330-56717345 chr3:56717330-56717348 chr3:56717330-56717345
49	CHD2	chr3:56716936-56717615	K562	blood:	n/a	n/a
50	POLR2A	chr3:56716126-56717626	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:56705021..56708606-chr3:56714722..56718211,5	MCF-7	breast:
2	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
3	chr3:56702147..56705420-chr3:56716741..56719178,3	MCF-7	breast:
4	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
5	chr3:56716275..56717973-chr3:56833928..56836671,2	K562	blood:
6	chr3:56715514..56718317-chr3:56833414..56836251,4	MCF-7	breast:

Variant related genes	Relation type
FAM208A	TF binding region
ENSG00000163947	Chromatin interaction
ENSG00000163946	Chromatin interaction
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10222629	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1054092	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1054093	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130525	0.82[EUR][1000 genomes]
rs11130526	0.82[EUR][1000 genomes]
rs11130527	0.86[EUR][1000 genomes]
rs11130542	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11712664	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712799	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11719707	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719726	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1316647	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13317989	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388256	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17216747	0.81[ASN][1000 genomes]
rs1812347	0.86[EUR][1000 genomes]
rs1873256	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291498	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291500	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2317132	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282525	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282530	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282531	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282542	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3172355	0.93[ASN][1000 genomes]
rs3732505	0.89[ASN][1000 genomes]
rs4681726	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681738	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681739	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4681903	0.89[ASN][1000 genomes]
rs4681904	0.85[ASN][1000 genomes]
rs4681937	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681955	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4682001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682008	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4974223	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4974225	0.82[EUR][1000 genomes]
rs55742226	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55810735	0.82[AMR][1000 genomes]
rs55828519	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56028632	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56172256	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56263252	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62251234	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445811	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6445812	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6556	0.89[ASN][1000 genomes]
rs6764730	0.86[EUR][1000 genomes]
rs6767903	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6794450	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72624856	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7612464	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7628343	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7633478	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7641898	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645941	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647095	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648297	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649872	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs873840	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311609	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311612	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs953540	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809117	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809741	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9814014	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9816100	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9816265	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819952	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9826788	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9830377	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834239	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9835134	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9841851	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847362	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861577	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864701	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9867302	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868059	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9871265	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9872059	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881152	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9883842	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327056	chr3:56715937-56718485	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1565378	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs1565378	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56713600-56717600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:56714800-56717600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:56715200-56717600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:56715200-56717800	Active TSS	Thymus	Thymus
5	chr3:56715400-56717600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:56715400-56717600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr3:56715400-56717600	Active TSS	NHLF	lung
8	chr3:56715600-56718000	Active TSS	Brain Angular Gyrus	brain
9	chr3:56715600-56718000	Active TSS	HSMMtube	muscle
10	chr3:56715800-56717600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:56715800-56717600	Active TSS	Hela-S3	cervix
12	chr3:56715800-56717800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:56715800-56717800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:56715800-56718000	Active TSS	Brain Hippocampus Middle	brain
15	chr3:56715800-56718000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:56716000-56717600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:56716000-56717600	Active TSS	Placenta Amnion	Placenta Amnion
18	chr3:56716000-56717800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:56716000-56717800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:56716000-56717800	Active TSS	Colonic Mucosa	Colon
21	chr3:56716000-56717800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr3:56716000-56717800	Active TSS	Fetal Brain Female	brain
23	chr3:56716000-56717800	Active TSS	Fetal Lung	lung
24	chr3:56716000-56717800	Active TSS	Psoas Muscle	Psoas
25	chr3:56716200-56717600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr3:56716200-56717600	Active TSS	Duodenum Mucosa	Duodenum
27	chr3:56716200-56717600	Active TSS	Gastric	stomach
28	chr3:56716200-56717600	Active TSS	Left Ventricle	heart
29	chr3:56716200-56717600	Active TSS	Ovary	ovary
30	chr3:56716200-56717600	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr3:56716200-56717600	Active TSS	Stomach Mucosa	stomach
32	chr3:56716200-56717800	Active TSS	Pancreas	Pancrea
33	chr3:56716200-56717800	Active TSS	Rectal Smooth Muscle	rectum
34	chr3:56716400-56717600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:56716400-56717600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:56716400-56717600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:56716400-56717600	Active TSS	Brain Anterior Caudate	brain
38	chr3:56716400-56717800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:56716400-56717800	Active TSS	Primary T cells from cord blood	blood
40	chr3:56716400-56717800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:56716400-56717800	Active TSS	Brain Substantia Nigra	brain
42	chr3:56716400-56717800	Active TSS	Fetal Kidney	kidney
43	chr3:56716400-56717800	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr3:56716400-56717800	Active TSS	Osteobl	bone
45	chr3:56716800-56717600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:56716800-56717600	Weak transcription	Fetal Heart	heart
47	chr3:56716800-56717800	Active TSS	Right Atrium	heart
48	chr3:56717200-56717600	Active TSS	Primary hematopoietic stem cells	blood
49	chr3:56717200-56717600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr3:56717200-56717800	Active TSS	Primary hematopoietic stem cells short term culture	blood

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