Variant report

Variant	rs6784203
Chromosome Location	chr3:49381678-49381679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr3:49381334-49381683	HepG2	liver:	n/a	n/a
2	FOXA1	chr3:49381282-49381765	HepG2	liver:	n/a	n/a
3	ARID3A	chr3:49381385-49381723	HepG2	liver:	n/a	n/a
4	FOXA1	chr3:49381341-49381768	HepG2	liver:	n/a	n/a
5	MYBL2	chr3:49381253-49381788	HepG2	liver:	n/a	n/a
6	MYBL2	chr3:49381219-49381724	HepG2	liver:	n/a	n/a
7	HNF4A	chr3:49381374-49381701	HepG2	liver:	n/a	n/a
8	FOXA1	chr3:49381259-49381707	HepG2	liver:	n/a	n/a
9	HNF4G	chr3:49381390-49381680	HepG2	liver:	n/a	n/a
10	EP300	chr3:49381260-49381711	HepG2	liver:	n/a	n/a
11	FOXA1	chr3:49381262-49381744	HepG2	liver:	n/a	n/a
12	EP300	chr3:49381292-49381710	HepG2	liver:	n/a	n/a
13	TBP	chr3:49381360-49381698	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:62501751..62503501-chr3:49379997..49382332,2	MCF-7	breast:
2	chr3:49377677..49379380-chr3:49380905..49382983,2	K562	blood:
3	chr3:49376333..49378234-chr3:49381279..49382912,2	MCF-7	breast:

No data

Variant related genes	Relation type
USP4	TF binding region
ENSG00000258890	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000108654	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10155014	0.89[EUR][1000 genomes]
rs1106620	0.83[EUR][1000 genomes]
rs11130190	0.96[EUR][1000 genomes]
rs11710434	0.87[EUR][1000 genomes]
rs11715060	0.85[EUR][1000 genomes]
rs11719762	0.95[EUR][1000 genomes]
rs11720542	0.87[EUR][1000 genomes]
rs11720657	0.96[EUR][1000 genomes]
rs13096474	0.89[EUR][1000 genomes]
rs1464569	0.87[EUR][1000 genomes]
rs2140270	0.90[EUR][1000 genomes]
rs2177268	0.90[EUR][1000 genomes]
rs2329025	0.83[EUR][1000 genomes]
rs3448	0.96[EUR][1000 genomes]
rs4955413	0.89[EUR][1000 genomes]
rs4955424	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4955425	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4955430	0.96[EUR][1000 genomes]
rs56127630	0.90[EUR][1000 genomes]
rs57273516	0.82[EUR][1000 genomes]
rs62259933	0.86[EUR][1000 genomes]
rs62259943	0.91[EUR][1000 genomes]
rs62259944	0.89[EUR][1000 genomes]
rs62259947	0.90[EUR][1000 genomes]
rs62261183	0.81[EUR][1000 genomes]
rs6446262	0.94[EUR][1000 genomes]
rs6446275	0.86[EUR][1000 genomes]
rs6769744	0.95[EUR][1000 genomes]
rs6775069	0.93[EUR][1000 genomes]
rs6783003	0.81[EUR][1000 genomes]
rs6785045	0.90[EUR][1000 genomes]
rs6790105	0.83[EUR][1000 genomes]
rs6796147	0.90[EUR][1000 genomes]
rs6805609	0.85[EUR][1000 genomes]
rs6809204	0.91[EUR][1000 genomes]
rs72934271	0.81[EUR][1000 genomes]
rs73088137	0.89[EUR][1000 genomes]
rs7355800	0.81[EUR][1000 genomes]
rs7613491	0.82[EUR][1000 genomes]
rs7619789	0.82[EUR][1000 genomes]
rs7620024	0.89[EUR][1000 genomes]
rs7638750	0.83[EUR][1000 genomes]
rs7647973	0.82[EUR][1000 genomes]
rs7648995	0.90[EUR][1000 genomes]
rs8897	0.87[EUR][1000 genomes]
rs940045	0.88[EUR][1000 genomes]
rs974495	0.95[EUR][1000 genomes]
rs9812360	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9817807	0.89[EUR][1000 genomes]
rs9834535	0.81[EUR][1000 genomes]
rs9842132	0.91[EUR][1000 genomes]
rs9860055	0.83[EUR][1000 genomes]
rs9860285	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9861027	0.90[EUR][1000 genomes]
rs9881860	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6784203	AMT	cis	Esophagus Mucosa	GTEx
rs6784203	WDR6	cis	Nerve Tibial	GTEx
rs6784203	NICN1-AS1	cis	Thyroid	GTEx
rs6784203	AMT	cis	lung	GTEx
rs6784203	WDR6	cis	Muscle Skeletal	GTEx
rs6784203	AMT	cis	Muscle Skeletal	GTEx
rs6784203	AMT	cis	Thyroid	GTEx
rs6784203	AMT	cis	Nerve Tibial	GTEx
rs6784203	AMT	cis	Adipose Subcutaneous	GTEx
rs6784203	AMT	cis	Artery Tibial	GTEx
rs6784203	NICN1	cis	Thyroid	GTEx
rs6784203	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs6784203	AMT	cis	Esophagus Muscularis	GTEx
rs6784203	AMT	cis	Whole Blood	GTEx
rs6784203	AMT	cis	Artery Aorta	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49378400-49382400	Enhancers	Primary B cells from peripheral blood	blood
2	chr3:49378600-49382000	Enhancers	Primary hematopoietic stem cells	blood
3	chr3:49378600-49382000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:49378600-49382000	Weak transcription	NHDF-Ad	bronchial
5	chr3:49378600-49382400	Weak transcription	Osteobl	bone
6	chr3:49378600-49382600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:49378600-49382600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:49378600-49382600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:49378600-49382600	Weak transcription	NH-A	brain
10	chr3:49378600-49383800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:49378600-49383800	Weak transcription	NHEK	skin
12	chr3:49378600-49384000	Weak transcription	NHLF	lung
13	chr3:49378600-49384200	Weak transcription	HSMMtube	muscle
14	chr3:49378600-49384400	Weak transcription	Psoas Muscle	Psoas
15	chr3:49378600-49385200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:49378600-49386400	Weak transcription	K562	blood
17	chr3:49378600-49386600	Weak transcription	Stomach Mucosa	stomach
18	chr3:49378600-49386800	Weak transcription	Gastric	stomach
19	chr3:49378600-49388400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:49378600-49388800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:49378600-49388800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:49378600-49390000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:49378600-49392000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:49378800-49381800	Weak transcription	HUVEC	blood vessel
25	chr3:49378800-49382000	Weak transcription	Hela-S3	cervix
26	chr3:49378800-49382600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:49378800-49382600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:49378800-49382600	Weak transcription	HMEC	breast
29	chr3:49378800-49383400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:49378800-49383800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:49378800-49384000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:49378800-49384200	Enhancers	Adipose Nuclei	Adipose
33	chr3:49378800-49386800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:49378800-49387400	Weak transcription	Esophagus	oesophagus
35	chr3:49379000-49383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:49379000-49384200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:49379000-49385800	Weak transcription	Fetal Intestine Large	intestine
38	chr3:49379000-49385800	Weak transcription	Fetal Intestine Small	intestine
39	chr3:49379000-49392000	Weak transcription	Left Ventricle	heart
40	chr3:49379400-49384000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:49379600-49381800	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:49379600-49382200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:49379600-49382200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:49379600-49382400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:49379600-49382600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:49379600-49382600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:49379600-49384000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:49379600-49384200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:49379600-49384200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:49379800-49386600	Weak transcription	Stomach Smooth Muscle	stomach

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