Variant report

Variant	rs3749282
Chromosome Location	chr3:145783440-145783441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:181)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:181 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:145783273-145783714	T-47D	breast:	n/a	n/a
2	CTCF	chr3:145783158-145783835	HCT-116	colon:	n/a	n/a
3	RFX5	chr3:145783303-145783890	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr3:145783226-145783649	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:145783400-145783550	K562	blood:	n/a	n/a
6	RAD21	chr3:145783314-145783654	GM12878	blood:	n/a	n/a
7	FOXA1	chr3:145783260-145783704	T-47D	breast:	n/a	n/a
8	CTCF	chr3:145783420-145783570	HMF	breast:	n/a	n/a
9	CTCF	chr3:145783351-145783617	HepG2	liver:	n/a	n/a
10	CTCF	chr3:145783397-145783611	K562	blood:	n/a	n/a
11	CTCF	chr3:145783420-145783570	HCT-116	colon:	n/a	n/a
12	CTCF	chr3:145783357-145783576	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr3:145783316-145783617	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr3:145783346-145783626	Spleen_OC	spleen:	n/a	n/a
15	CTCF	chr3:145783400-145783550	GM12878	blood:	n/a	n/a
16	CTCF	chr3:145783400-145783550	AG10803	skin:	n/a	n/a
17	RAD21	chr3:145783351-145783667	A549	lung:	n/a	n/a
18	RAD21	chr3:145783221-145783695	HCT-116	colon:	n/a	n/a
19	CTCF	chr3:145783360-145783510	NHEK	skin:	n/a	n/a
20	JUN	chr3:145783293-145783657	K562	blood:	n/a	n/a
21	CTCF	chr3:145783380-145783530	HRE	kidney:	n/a	n/a
22	CTCF	chr3:145783400-145783550	SAEC	small airway:	n/a	n/a
23	JUND	chr3:145783403-145783670	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr3:145783440-145783590	HA-sp	spinal cord:	n/a	n/a
25	CTCF	chr3:145783393-145783602	Hela-S3	cervix:	n/a	n/a
26	MYC	chr3:145783393-145783746	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:145783351-145784586	HepG2	liver:	n/a	n/a
28	CTCF	chr3:145783420-145783570	AG10803	skin:	n/a	n/a
29	CTCF	chr3:145783440-145783590	RPTEC	kidney:	n/a	n/a
30	RAD21	chr3:145783222-145783810	HCT-116	colon:	n/a	n/a
31	STAT3	chr3:145783385-145783559	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr3:145783400-145783550	HA-sp	spinal cord:	n/a	n/a
33	CTCF	chr3:145783420-145783570	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:145783379-145783585	A549	lung:	n/a	n/a
35	CTCF	chr3:145783400-145783550	HPF	lung:	n/a	n/a
36	CTCF	chr3:145783320-145783470	NHDF-neo	bronchial:	n/a	n/a
37	FOXA1	chr3:145783271-145783694	HepG2	liver:	n/a	n/a
38	CTCF	chr3:145783440-145783590	GM12872	blood:	n/a	n/a
39	CTCF	chr3:145783380-145783530	HCPEpiC	choroid plexus:	n/a	n/a
40	CTCF	chr3:145783380-145783530	HUVEC	blood vessel:	n/a	n/a
41	CEBPB	chr3:145783351-145783625	HepG2	liver:	n/a	n/a
42	CTCF	chr3:145783440-145783590	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr3:145783380-145783530	GM12872	blood:	n/a	n/a
44	CTCF	chr3:145783384-145783604	GM10248	blood:	n/a	n/a
45	CTCF	chr3:145783440-145783590	HEK293	kidney:	n/a	n/a
46	CTCF	chr3:145783386-145783604	GM12878	blood:	n/a	n/a
47	ARID3A	chr3:145783331-145783735	HepG2	liver:	n/a	n/a
48	CTCF	chr3:145783420-145783570	HEEpiC	esophagus:	n/a	n/a
49	SMC3	chr3:145783280-145783690	GM12878	blood:	n/a	n/a
50	RAD21	chr3:145783317-145783691	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:145782122..145785411-chr3:145878106..145882365,5	MCF-7	breast:
2	chr3:145783012..145783944-chr3:146295169..146296067,2	K562	blood:
3	chr3:145783058..145783996-chr3:145865459..145867166,7	MCF-7	breast:
4	chr3:145783270..145783989-chr3:145904824..145905816,4	MCF-7	breast:
5	chr3:145783076..145784215-chr3:145904959..145906020,4	MCF-7	breast:
6	chr3:145779679..145784840-chr3:145877412..145880527,5	MCF-7	breast:
7	chr3:145783388..145783946-chr3:145902245..145902938,2	MCF-7	breast:
8	chr3:145783014..145783624-chr3:145865958..145866776,2	MCF-7	breast:
9	chr3:145783038..145783586-chr3:146044661..146045578,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261051	TF binding region
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12632001	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2864794	0.87[ASW][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs3804659	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59384952	0.88[AFR][1000 genomes]
rs67406460	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67671074	0.85[AFR][1000 genomes]
rs6787634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73010484	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642145	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9842865	0.82[EUR][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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3749282	PLOD2	cis	lymphoblastoid	seeQTL
rs3749282	PLSCR4	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145762800-145785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:145768800-145788400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:145773800-145783600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:145774600-145787200	Weak transcription	Esophagus	oesophagus
5	chr3:145774600-145795400	Weak transcription	Aorta	Aorta
6	chr3:145775400-145786600	Weak transcription	HepG2	liver
7	chr3:145776200-145786000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:145776200-145786400	Weak transcription	Adipose Nuclei	Adipose
9	chr3:145776600-145787200	Weak transcription	HMEC	breast
10	chr3:145776800-145783600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:145777000-145783600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:145777000-145783600	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:145777600-145783600	Strong transcription	Osteobl	bone
15	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
16	chr3:145778600-145789000	Weak transcription	Left Ventricle	heart
17	chr3:145778800-145788400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:145779000-145789600	Weak transcription	Fetal Heart	heart
19	chr3:145779400-145788800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:145779600-145784200	Strong transcription	HSMM	muscle
21	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
22	chr3:145780000-145783600	Weak transcription	Fetal Lung	lung
23	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:145780200-145784200	Weak transcription	NHLF	lung
25	chr3:145780600-145784200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
27	chr3:145780800-145786600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:145780800-145793800	Weak transcription	Ovary	ovary
29	chr3:145780800-145793800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:145781000-145783600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:145781000-145788400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:145781000-145788800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:145781800-145785000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
36	chr3:145782000-145785400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:145782600-145783600	Weak transcription	NHDF-Ad	bronchial
38	chr3:145782600-145786200	Weak transcription	Liver	Liver
39	chr3:145782600-145786400	Weak transcription	Fetal Intestine Large	intestine
40	chr3:145782800-145784600	Weak transcription	NH-A	brain
41	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
42	chr3:145783000-145783600	Weak transcription	A549	lung
43	chr3:145783000-145784400	Weak transcription	HSMMtube	muscle
44	chr3:145783000-145785000	Weak transcription	HUVEC	blood vessel
45	chr3:145783200-145785600	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr3:145783400-145783800	Active TSS	Pancreatic Islets	Pancreatic Islet

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