Variant report

Variant	rs56721759
Chromosome Location	chr3:112359740-112359741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:124)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:124 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112359734-112360334	K562	blood:	n/a	n/a
2	MAX	chr3:112358983-112360732	A549	lung:	n/a	chr3:112360464-112360473
3	POLR2A	chr3:112358726-112360545	SK-N-SH	brain:	n/a	n/a
4	MAX	chr3:112358802-112360786	SK-N-SH	brain:	n/a	chr3:112360464-112360473
5	CEBPB	chr3:112358594-112360673	A549	lung:	n/a	chr3:112358750-112358761
6	POLR2A	chr3:112359738-112360225	A549	lung:	n/a	n/a
7	PBX3	chr3:112359710-112360326	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr3:112359722-112360097	K562	blood:	n/a	n/a
9	POLR2A	chr3:112359596-112360338	K562	blood:	n/a	n/a
10	TCF12	chr3:112359737-112360287	A549	lung:	n/a	n/a
11	MAFK	chr3:112358924-112360416	Hela-S3	cervix:	n/a	chr3:112359917-112359932
12	MXI1	chr3:112359494-112360160	K562	blood:	n/a	n/a
13	SP1	chr3:112358971-112360621	A549	lung:	n/a	chr3:112359997-112360007
14	GATA3	chr3:112358736-112360473	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:112359738-112360281	GM12892	blood:	n/a	n/a
16	GATA3	chr3:112359598-112360297	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:112359588-112360334	K562	blood:	n/a	n/a
18	TAF7	chr3:112359712-112360311	K562	blood:	n/a	n/a
19	SMC3	chr3:112359043-112360546	Hela-S3	cervix:	n/a	n/a
20	ZBTB33	chr3:112359658-112360390	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr3:112359526-112360366	K562	blood:	n/a	n/a
22	POLR2A	chr3:112359590-112360239	K562	blood:	n/a	n/a
23	RFX5	chr3:112359075-112360492	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:112359734-112360198	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:112358884-112362166	IMR90	lung:	n/a	n/a
26	POLR2A	chr3:112359690-112360293	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:112358922-112360408	MCF10A-Er-Src	breast:	n/a	n/a
28	KAP1	chr3:112359019-112360794	HEK293	kidney:	n/a	n/a
29	POLR2A	chr3:112359675-112360278	GM12891	blood:	n/a	n/a
30	SP1	chr3:112359679-112360385	H1-hESC	embryonic stem cell:	n/a	chr3:112359997-112360007
31	POLR2A	chr3:112359641-112360383	HCT-116	colon:	n/a	n/a
32	NFIC	chr3:112358938-112360494	SK-N-SH	brain:	n/a	n/a
33	ZNF263	chr3:112359693-112360273	HEK293-T-REx	kidney:	n/a	n/a
34	TAF1	chr3:112359706-112360206	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr3:112359338-112360524	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr3:112359086-112360463	A549	lung:	n/a	n/a
37	ZBTB33	chr3:112359738-112360370	A549	lung:	n/a	n/a
38	POLR2A	chr3:112359056-112360566	HUVEC	blood vessel:	n/a	n/a
39	TEAD4	chr3:112359291-112360424	SK-N-SH	brain:	n/a	n/a
40	RCOR1	chr3:112359685-112360406	K562	blood:	n/a	n/a
41	TCF12	chr3:112358932-112360699	A549	lung:	n/a	n/a
42	HEY1	chr3:112359735-112360238	K562	blood:	n/a	n/a
43	SIN3AK20	chr3:112359090-112360526	SK-N-SH	brain:	n/a	n/a
44	RFX5	chr3:112359594-112360182	K562	blood:	n/a	n/a
45	EP300	chr3:112359603-112360460	A549	lung:	n/a	n/a
46	CHD2	chr3:112359382-112360219	K562	blood:	n/a	n/a
47	EP300	chr3:112359670-112360468	A549	lung:	n/a	n/a
48	POLR2A	chr3:112359683-112360317	SK-N-MC	brain:	n/a	n/a
49	ZBTB33	chr3:112359700-112360409	A549	lung:	n/a	n/a
50	POLR2A	chr3:112359662-112360301	K562	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112326392..112328017-chr3:112358236..112359844,2	MCF-7	breast:
2	chr3:112358576..112361067-chr3:112520655..112523598,3	MCF-7	breast:
3	chr3:112289268..112293035-chr3:112358216..112361029,3	MCF-7	breast:
4	chr3:112358478..112360877-chr3:112708365..112711089,3	MCF-7	breast:
5	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
6	chr3:112354638..112357493-chr3:112357624..112362114,5	K562	blood:
7	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
8	chr3:112357856..112364091-chr3:112692717..112699765,9	MCF-7	breast:
9	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
10	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
11	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
12	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
13	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
14	chr3:112359721..112360525-chr9:125675165..125676110,2	Hela-S3	cervix:
15	chr17:48784635..48785585-chr3:112359690..112360504,2	Hela-S3	cervix:
16	chr3:112358089..112359762-chr3:112460166..112463073,2	MCF-7	breast:
17	chr19:19030312..19031078-chr3:112359710..112360246,2	Hela-S3	cervix:
18	chr3:112359608..112361417-chr3:113001269..113003641,2	MCF-7	breast:
19	chr3:112011328..112014210-chr3:112359098..112361496,2	MCF-7	breast:
20	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
21	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:
22	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC80-1	chr3:112359613-112359885	NONHSAT091192

No data

Variant related genes	Relation type
CCDC80	TF binding region
ENSG00000144857	Chromatin interaction
ENSG00000105671	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000242770	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000186130	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000154945	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000163606	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000172139	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12634229	0.82[ASN][1000 genomes]
rs16859897	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16859911	0.97[ASN][1000 genomes]
rs16859916	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28364588	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28364589	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28364604	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7640793	0.87[AMR][1000 genomes];0.96[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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112354000-112360600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:112354800-112360000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr3:112355800-112360200	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr3:112356000-112360600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:112356200-112360000	Active TSS	Brain Substantia Nigra	brain
6	chr3:112357200-112360400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:112357200-112361000	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr3:112358000-112360400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:112358000-112360400	Active TSS	Right Ventricle	heart
10	chr3:112358400-112360400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:112358600-112360000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:112358600-112360000	Active TSS	Fetal Intestine Large	intestine
13	chr3:112358600-112360000	Active TSS	Placenta Amnion	Placenta Amnion
14	chr3:112358600-112360000	Active TSS	HSMMtube	muscle
15	chr3:112358600-112360200	Active TSS	Brain Hippocampus Middle	brain
16	chr3:112358600-112360200	Active TSS	Colon Smooth Muscle	Colon
17	chr3:112358600-112360400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:112358600-112360400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:112358600-112360400	ZNF genes & repeats	Fetal Brain Male	brain
20	chr3:112358600-112360400	Active TSS	HSMM	muscle
21	chr3:112358600-112360600	Flanking Active TSS	HUVEC	blood vessel
22	chr3:112358600-112361800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:112358600-112363200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:112358600-112365400	Weak transcription	Lung	lung
25	chr3:112358800-112359800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:112358800-112359800	Active TSS	Stomach Smooth Muscle	stomach
27	chr3:112358800-112359800	Flanking Active TSS	HMEC	breast
28	chr3:112358800-112360000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:112358800-112360000	Active TSS	Muscle Satellite Cultured Cells	--
30	chr3:112358800-112360000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:112358800-112360000	Active TSS	Fetal Muscle Trunk	muscle
32	chr3:112358800-112360000	Active TSS	Osteobl	bone
33	chr3:112358800-112360200	Active TSS	Fetal Stomach	stomach
34	chr3:112358800-112360200	Active TSS	NHLF	lung
35	chr3:112358800-112360400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:112358800-112360400	Active TSS	Ovary	ovary
37	chr3:112358800-112360400	Active TSS	Right Atrium	heart
38	chr3:112358800-112360400	Active TSS	NHDF-Ad	bronchial
39	chr3:112358800-112363200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:112359000-112359800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:112359000-112359800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:112359000-112359800	Active TSS	Brain Anterior Caudate	brain
43	chr3:112359000-112359800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:112359000-112359800	Active TSS	Fetal Muscle Leg	muscle
45	chr3:112359000-112360000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:112359000-112360000	Active TSS	NH-A	brain
47	chr3:112359000-112360200	Active TSS	Aorta	Aorta
48	chr3:112359000-112360200	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:112359000-112360400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:112359000-112360400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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