Variant report

Variant	rs56741529
Chromosome Location	chr3:69373647-69373648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:164)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:164 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:69373600-69373750	HCT-116	colon:	n/a	n/a
2	CTCF	chr3:69373596-69373831	GM12892	blood:	n/a	n/a
3	CTCF	chr3:69373548-69373872	K562	blood:	n/a	n/a
4	CTCF	chr3:69373560-69373710	NHDF-neo	bronchial:	n/a	n/a
5	CTCF	chr3:69373560-69373710	HFF-Myc	foreskin:	n/a	n/a
6	CTCF	chr3:69373600-69373750	GM12867	blood:	n/a	n/a
7	CTCF	chr3:69373564-69373811	HepG2	liver:	n/a	n/a
8	CTCF	chr3:69373603-69373790	Fibrobl	skin:	n/a	n/a
9	CTCF	chr3:69373625-69373775	GM13976	blood:	n/a	n/a
10	CTCF	chr3:69373600-69373750	GM12864	blood:	n/a	n/a
11	SMC3	chr3:69373240-69373919	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr3:69373540-69373690	HUVEC	blood vessel:	n/a	n/a
13	CTCF	chr3:69373637-69373786	Pancreas_OC	pancreas:	n/a	n/a
14	CTCF	chr3:69373619-69373803	MCF-7	breast:	n/a	n/a
15	CTCF	chr3:69373593-69373757	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr3:69373600-69373750	Caco-2	colon:	n/a	n/a
17	CTCF	chr3:69373442-69374019	A549	lung:	n/a	n/a
18	CTCF	chr3:69373620-69373770	NHEK	skin:	n/a	n/a
19	CTCF	chr3:69373514-69373800	HepG2	liver:	n/a	n/a
20	RAD21	chr3:69373563-69373937	A549	lung:	n/a	n/a
21	CTCF	chr3:69373640-69373790	GM12864	blood:	n/a	n/a
22	RAD21	chr3:69373626-69373771	K562	blood:	n/a	n/a
23	CTCF	chr3:69373620-69373770	HBMEC	blood vessel:	n/a	n/a
24	RAD21	chr3:69373455-69373988	HCT-116	colon:	n/a	n/a
25	CTCF	chr3:69373640-69373790	GM12865	blood:	n/a	n/a
26	CTCF	chr3:69373640-69373790	GM12872	blood:	n/a	n/a
27	CTCF	chr3:69373589-69373811	Medullo	brain:	n/a	n/a
28	CTCF	chr3:69373620-69373770	HVMF	connective:	n/a	n/a
29	CTCF	chr3:69373468-69373907	MCF-7	breast:	n/a	n/a
30	RAD21	chr3:69373283-69373933	GM12878	blood:	n/a	n/a
31	CTCF	chr3:69373506-69373939	HCT-116	colon:	n/a	n/a
32	CTCF	chr3:69373600-69373750	WERI-Rb-1	eye:	n/a	n/a
33	ZNF384	chr3:69373612-69373962	GM12878	blood:	n/a	n/a
34	CTCF	chr3:69373640-69373790	GM12871	blood:	n/a	n/a
35	CTCF	chr3:69373561-69373827	MCF-7	breast:	n/a	n/a
36	RAD21	chr3:69373472-69373936	GM12878	blood:	n/a	n/a
37	ZNF143	chr3:69373524-69373872	GM12878	blood:	n/a	n/a
38	EBF1	chr3:69373275-69374078	GM12878	blood:	n/a	chr3:69373749-69373760
39	FOXM1	chr3:69373488-69373936	GM12878	blood:	n/a	n/a
40	CTCF	chr3:69373620-69373770	HEK293	kidney:	n/a	n/a
41	CTCF	chr3:69373580-69373730	MCF-7	breast:	n/a	n/a
42	CTCF	chr3:69373600-69373780	HUVEC	blood vessel:	n/a	n/a
43	CTCF	chr3:69373560-69373710	HEK293	kidney:	n/a	n/a
44	CTCF	chr3:69373612-69373788	ProgFib	skin:	n/a	n/a
45	RAD21	chr3:69372998-69374079	SK-N-SH	brain:	n/a	n/a
46	RAD21	chr3:69373496-69373949	A549	lung:	n/a	n/a
47	CTCF	chr3:69373458-69374067	SK-N-SH	brain:	n/a	n/a
48	CTCF	chr3:69373616-69373796	LNCaP	prostate:	n/a	n/a
49	RAD21	chr3:69373535-69373870	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr3:69373618-69373786	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:69373351..69374005-chr3:69474320..69475043,3	MCF-7	breast:
2	chr3:69373310..69374161-chr3:69459043..69460191,4	MCF-7	breast:
3	chr3:69373390..69375436-chr3:69478207..69481106,2	MCF-7	breast:
4	chr3:69371696..69374410-chr3:69474254..69475900,2	MCF-7	breast:
5	chr3:69373623..69374172-chr3:69458720..69460070,3	MCF-7	breast:

No data

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10865649	0.84[ASN][1000 genomes]
rs11707811	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492029	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1564757	0.82[ASN][1000 genomes]
rs17005615	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2170800	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35331889	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4290808	0.83[ASN][1000 genomes]
rs4428187	0.83[ASN][1000 genomes]
rs4855308	0.85[ASN][1000 genomes]
rs4855389	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56119799	0.87[EUR][1000 genomes]
rs56336456	0.83[ASN][1000 genomes]
rs59563257	0.83[ASN][1000 genomes]
rs6549203	0.83[ASN][1000 genomes]
rs6774274	0.83[ASN][1000 genomes]
rs6776474	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67846536	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67940491	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7612526	0.82[ASN][1000 genomes]
rs7617464	0.82[ASN][1000 genomes]
rs9310148	0.82[ASN][1000 genomes]
rs9861135	0.83[ASN][1000 genomes]
rs9868217	0.82[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	nsv876935	chr3:69307942-69401248	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69350000-69374200	Weak transcription	Aorta	Aorta
2	chr3:69360600-69382200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:69366400-69376200	Enhancers	Brain Anterior Caudate	brain
4	chr3:69366800-69378200	Enhancers	Brain Hippocampus Middle	brain
5	chr3:69367200-69378400	Enhancers	Brain Substantia Nigra	brain
6	chr3:69367400-69374800	Enhancers	Brain Angular Gyrus	brain
7	chr3:69368400-69378200	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:69369000-69377600	Weak transcription	Fetal Brain Female	brain
9	chr3:69369800-69376600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:69370200-69384000	Weak transcription	Left Ventricle	heart
11	chr3:69370400-69376600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:69370400-69379200	Weak transcription	Spleen	Spleen
13	chr3:69370600-69375800	Weak transcription	HUVEC	blood vessel
14	chr3:69370800-69373800	Weak transcription	Thymus	Thymus
15	chr3:69371000-69373800	Enhancers	Placenta	Placenta
16	chr3:69371000-69375600	Weak transcription	Fetal Lung	lung
17	chr3:69371000-69377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:69371400-69377000	Weak transcription	Fetal Stomach	stomach
19	chr3:69371600-69375600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:69371800-69380000	Weak transcription	Fetal Heart	heart
21	chr3:69372000-69373800	Enhancers	HSMM	muscle
22	chr3:69372000-69375000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:69372200-69377400	Weak transcription	Ovary	ovary
24	chr3:69372200-69403800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:69372400-69374400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:69372400-69377200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:69372400-69380000	Weak transcription	NHEK	skin
28	chr3:69372800-69374800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr3:69373000-69375000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:69373000-69375800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:69373000-69376000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:69373200-69373800	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:69373200-69373800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr3:69373200-69374400	Enhancers	Dnd41	blood
35	chr3:69373200-69374600	Enhancers	Lung	lung
36	chr3:69373200-69374600	Enhancers	Right Atrium	heart
37	chr3:69373200-69375800	Enhancers	Primary B cells from cord blood	blood
38	chr3:69373400-69374200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr3:69373400-69374400	Weak transcription	Adipose Nuclei	Adipose
40	chr3:69373400-69375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:69373400-69375400	Enhancers	GM12878-XiMat	blood
42	chr3:69373400-69376200	Enhancers	Fetal Thymus	thymus
43	chr3:69373600-69374200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:69373600-69374400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:69373600-69375400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:69373600-69375400	Weak transcription	HSMMtube	muscle
47	chr3:69373600-69377400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:69373600-69378400	Enhancers	Primary B cells from peripheral blood	blood

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