Variant report

Variant	rs62255965
Chromosome Location	chr3:56591208-56591209
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:358)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:358 , 50 per page) page: 1 2 3 4 5 6 7 8

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	POLR2A	chr3:56590793-56591766	Hela-S3	cervix:	n/a	n/a
3	MAZ	chr3:56590848-56592052	GM12878	blood:	n/a	n/a
4	HMGN3	chr3:56591000-56591380	K562	blood:	n/a	n/a
5	GTF2F1	chr3:56590904-56592042	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr3:56590960-56591442	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:56590763-56591893	K562	blood:	n/a	n/a
8	TAF1	chr3:56590896-56591590	H1-neurons	neurons:	n/a	n/a
9	REST	chr3:56590979-56591343	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:56590857-56591799	K562	blood:	n/a	n/a
11	FOXP2	chr3:56590923-56591367	PFSK-1	brain:	n/a	n/a
12	RFX5	chr3:56591005-56591334	GM12878	blood:	n/a	chr3:56591142-56591151
13	POLR2A	chr3:56590652-56591773	Raji	blood:	n/a	n/a
14	KAP1	chr3:56591012-56592291	HEK293	kidney:	n/a	n/a
15	E2F4	chr3:56590978-56592027	MCF10A-Er-Src	breast:	n/a	n/a
16	CHD1	chr3:56590763-56591987	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF1	chr3:56590860-56591463	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:56590681-56591598	U87	brain:	n/a	n/a
19	FOXA2	chr3:56591011-56591461	A549	lung:	n/a	n/a
20	ZNF384	chr3:56590932-56591250	K562	blood:	n/a	n/a
21	ZNF143	chr3:56590988-56591327	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:56590779-56591935	GM12878	blood:	n/a	n/a
23	MYC	chr3:56590883-56592018	K562	blood:	n/a	n/a
24	POLR2A	chr3:56590721-56591575	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:56590848-56591451	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr3:56590764-56591427	PANC-1	pancreas:	n/a	n/a
27	MAFK	chr3:56591028-56591252	K562	blood:	n/a	n/a
28	POLR2A	chr3:56590900-56591560	HUVEC	blood vessel:	n/a	n/a
29	TAF1	chr3:56590830-56591464	A549	lung:	n/a	n/a
30	NFYB	chr3:56590958-56591584	Hela-S3	cervix:	n/a	chr3:56591139-56591154 chr3:56591140-56591154 chr3:56591141-56591156 chr3:56591139-56591154 chr3:56591142-56591152
31	JUND	chr3:56590943-56591356	A549	lung:	n/a	n/a
32	CTCF	chr3:56591066-56592085	GM12878	blood:	n/a	n/a
33	TEAD4	chr3:56590851-56591295	H1-hESC	embryonic stem cell:	n/a	n/a
34	SMC3	chr3:56590931-56591921	Hela-S3	cervix:	n/a	chr3:56591610-56591620
35	POLR2A	chr3:56590884-56591379	HepG2	liver:	n/a	n/a
36	TBP	chr3:56590927-56592299	Hela-S3	cervix:	n/a	n/a
37	BRCA1	chr3:56590978-56591890	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:56590843-56591426	SK-N-MC	brain:	n/a	n/a
39	E2F6	chr3:56590933-56591351	A549	lung:	n/a	n/a
40	CHD2	chr3:56590971-56591918	K562	blood:	n/a	n/a
41	CBX3	chr3:56590923-56591423	K562	blood:	n/a	n/a
42	POLR2A	chr3:56590759-56591559	MCF-7	breast:	n/a	n/a
43	TCF12	chr3:56590829-56591757	ECC-1	luminal epithelium:	n/a	n/a
44	MXI1	chr3:56590612-56592100	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:56590710-56591500	HUVEC	blood vessel:	n/a	n/a
46	FOXM1	chr3:56591004-56591721	GM12878	blood:	n/a	n/a
47	ZKSCAN1	chr3:56591001-56591861	Hela-S3	cervix:	n/a	n/a
48	MAX	chr3:56590933-56591900	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr3:56590638-56591604	PFSK-1	brain:	n/a	n/a
50	MAX	chr3:56590807-56591895	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:56591190-56591240	LNCaP	prostate:	n/a
2	chr3:56591190-56591240	RPTEC	kidney:	n/a
3	chr3:56591190-56591240	SK-N-SH_RA	brain:	n/a
4	chr3:56591190-56591240	GM12891	blood:	n/a
5	chr3:56591190-56591240	Hela-S3	cervix:	n/a
6	chr3:56591190-56591240	Hepatocyte	liver:	n/a
7	chr3:56591190-56591240	BE2_C	brain:	n/a
8	chr3:56591190-56591240	GM19239	blood:	n/a
9	chr3:56591190-56591240	ECC-1	luminal epithelium:	n/a
10	chr3:56591190-56591240	A549	lung:	n/a
11	chr3:56591190-56591240	HRPEpiC	eye:	n/a
12	chr3:56591190-56591240	NT2-D1	testis:	n/a
13	chr3:56591190-56591240	HCF	heart:	n/a
14	chr3:56591190-56591240	HMEC	breast:	n/a
15	chr3:56591190-56591240	AoSMC	blood vessel:	n/a
16	chr3:56591190-56591240	T-47D	breast:	n/a
17	chr3:56591190-56591240	HIPEpiC	eye:	n/a
18	chr3:56591190-56591240	NHDF-neo	bronchial:	n/a
19	chr3:56591190-56591240	HEK293	kidney:	embryo
20	chr3:56591190-56591240	GM12878	blood:	n/a
21	chr3:56591190-56591240	GM12892	blood:	n/a
22	chr3:56591190-56591240	H1-hESC	embryonic stem cell:	embryo
23	chr3:56591190-56591240	HRE	kidney:	n/a
24	chr3:56591190-56591240	MCF-7	breast:	n/a
25	chr3:56591190-56591240	PFSK-1	brain:	n/a
26	chr3:56591190-56591240	SKMC	muscle:	n/a
27	chr3:56591190-56591240	NH-A	brain:	n/a
28	chr3:56591190-56591240	Jurkat	blood:	n/a
29	chr3:56591190-56591240	HAEpiC	amniotic membrane:	n/a
30	chr3:56591190-56591240	HCM	heart:	n/a
31	chr3:56591190-56591240	CMK	blood:	n/a
32	chr3:56591190-56591240	HPAEpiC	pulmonary alveolar:	n/a
33	chr3:56591190-56591240	AG04449	skin:	fetal
34	chr3:56591190-56591240	AG10803	skin:	n/a
35	chr3:56591190-56591240	HEEpiC	esophagus:	n/a
36	chr3:56591190-56591240	BJ	skin:	n/a
37	chr3:56591190-56591240	MCF10A-Er-Src	breast:	n/a
38	chr3:56591190-56591240	HL-60	blood:	n/a
39	chr3:56591190-56591240	HepG2	liver:	n/a
40	chr3:56591190-56591240	PrEC	prostate:	n/a
41	chr3:56591190-56591240	IMR90	lung:	fetal
42	chr3:56591190-56591240	HCPEpiC	choroid plexus:	n/a
43	chr3:56591190-56591240	NHBE	bronchial:	n/a
44	chr3:56591190-56591240	Caco-2	colon:	n/a
45	chr3:56591190-56591240	AG04450	lung:	fetal
46	chr3:56591190-56591240	PANC-1	pancreas:	n/a
47	chr3:56591190-56591240	HNPCEpiC	eye:	n/a
48	chr3:56591190-56591240	HCT-116	colon:	n/a
49	chr3:56591190-56591240	SK-N-MC	brain:	n/a
50	chr3:56591190-56591240	ProgFib	skin:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
2	chr11:85375746..85376542-chr3:56590683..56591527,2	Hela-S3	cervix:
3	chr3:56588808..56592620-chr3:56662133..56663692,3	K562	blood:
4	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
5	chr17:61042877..61045351-chr3:56589650..56591304,2	MCF-7	breast:
6	chr3:56591141..56591731-chr7:66766903..66767777,2	Hela-S3	cervix:
7	chr3:56589716..56592620-chr3:56662133..56663652,2	K562	blood:

No data

Variant related genes	Relation type
CCDC66	TF binding region
CCDC66	CpG island
ENSG00000067601	Chromatin interaction
ENSG00000137504	Chromatin interaction
ENSG00000263931	Chromatin interaction
ENSG00000163946	Chromatin interaction
ENSG00000106610	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11130522	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1388252	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491162	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491167	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17216678	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17216712	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17216754	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17288866	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17288873	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306930	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306931	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41276465	0.84[ASN][1000 genomes]
rs41276467	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41276469	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4292200	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56758331	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57861120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58457441	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59835031	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59897254	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60606369	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61456176	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61654248	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61747994	0.92[EUR][1000 genomes]
rs62249737	0.92[EUR][1000 genomes]
rs62251182	0.85[EUR][1000 genomes]
rs62251183	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251186	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62251188	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251190	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251192	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251193	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251197	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251228	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251229	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251230	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251233	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251235	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251238	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251239	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251241	0.84[ASN][1000 genomes]
rs62251244	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62251245	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62254329	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255966	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255969	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255970	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255971	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255973	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255974	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62255977	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62255978	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62255980	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62255981	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256011	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256013	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256014	0.92[EUR][1000 genomes]
rs62256017	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256018	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256019	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256020	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256022	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62256023	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6782254	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788512	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6802548	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6810125	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73075746	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73081816	0.85[EUR][1000 genomes]
rs73081836	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73081850	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73083715	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73083725	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7635945	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs955247	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[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

No data

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	chr3:56590200-56591800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:56590200-56592000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:56590200-56592000	Active TSS	Duodenum Mucosa	Duodenum
5	chr3:56590200-56592000	Active TSS	Fetal Heart	heart
6	chr3:56590200-56592000	Active TSS	Fetal Kidney	kidney
7	chr3:56590200-56592600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:56590200-56592600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:56590200-56592600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr3:56590200-56592600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:56590400-56591400	Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr3:56590400-56591400	Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr3:56590400-56591400	Active TSS	Adipose Nuclei	Adipose
14	chr3:56590400-56591800	Active TSS	Primary monocytes fromperipheralblood	blood
15	chr3:56590400-56591800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:56590400-56591800	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr3:56590400-56591800	Active TSS	Liver	Liver
18	chr3:56590400-56591800	Active TSS	Brain Substantia Nigra	brain
19	chr3:56590400-56591800	Active TSS	Colon Smooth Muscle	Colon
20	chr3:56590400-56591800	Active TSS	Fetal Brain Male	brain
21	chr3:56590400-56591800	Active TSS	Fetal Lung	lung
22	chr3:56590400-56591800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:56590400-56591800	Active TSS	Rectal Smooth Muscle	rectum
24	chr3:56590400-56591800	Active TSS	HSMMtube	muscle
25	chr3:56590400-56592000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:56590400-56592000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:56590400-56592000	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr3:56590400-56592000	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr3:56590400-56592000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr3:56590400-56592000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr3:56590400-56592000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:56590400-56592000	Active TSS	Brain Anterior Caudate	brain
33	chr3:56590400-56592000	Active TSS	Brain Cingulate Gyrus	brain
34	chr3:56590400-56592000	Active TSS	Brain Hippocampus Middle	brain
35	chr3:56590400-56592000	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr3:56590400-56592000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr3:56590400-56592000	Active TSS	Fetal Muscle Leg	muscle
38	chr3:56590400-56592000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr3:56590400-56592000	Active TSS	Psoas Muscle	Psoas
40	chr3:56590400-56592000	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr3:56590400-56592000	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:56590400-56592000	Active TSS	Hela-S3	cervix
43	chr3:56590400-56592000	Active TSS	NH-A	brain
44	chr3:56590400-56592000	Active TSS	Osteobl	bone
45	chr3:56590400-56592200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr3:56590400-56592200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:56590400-56592200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:56590400-56592200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:56590400-56592200	Active TSS	Fetal Intestine Large	intestine
50	chr3:56590400-56592200	Active TSS	Fetal Intestine Small	intestine

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