Variant report

Variant	rs773125
Chromosome Location	chr12:56394954-56394955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56394885-56395627	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56365099..56368915-chr12:56389537..56395397,5	K562	blood:
2	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:
3	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
4	chr12:56391225..56393452-chr12:56393825..56395799,2	K562	blood:

Variant related genes	Relation type
SUOX	TF binding region
ENSG00000139531	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000123411	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1081975	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1873914	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2048036	0.80[ASN][1000 genomes]
rs61937247	0.80[ASN][1000 genomes]
rs61937248	0.80[ASN][1000 genomes]
rs61937249	0.80[ASN][1000 genomes]
rs705698	0.80[ASN][1000 genomes]
rs705699	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs705700	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs705702	0.83[ASN][1000 genomes]
rs772920	0.83[ASN][1000 genomes]
rs773114	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Rheumatoid arthritis	24390342	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs773125	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs773125	SUOX	cis	Artery Tibial	GTEx
rs773125	SUOX	cis	Skin Sun Exposed Lower leg	GTEx
rs773125	RAB5B	cis	Muscle Skeletal	GTEx
rs773125	AC034102.1	cis	Muscle Skeletal	GTEx
rs773125	SUOX	cis	Thyroid	GTEx
rs773125	SUOX	cis	Nerve Tibial	GTEx
rs773125	SUOX	cis	Artery Aorta	GTEx
rs773125	DEFB124	trans	lymphoblastoid	RTeQTL
rs773125	SUOX	cis	lung	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56391600-56395800	Weak transcription	Aorta	Aorta
2	chr12:56391600-56397600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:56391600-56398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:56391600-56399000	Weak transcription	Primary T cells from cord blood	blood
5	chr12:56391600-56400800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:56391800-56395800	Weak transcription	Esophagus	oesophagus
7	chr12:56391800-56396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:56391800-56396200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:56391800-56396200	Weak transcription	NHLF	lung
10	chr12:56391800-56396400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56391800-56397000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:56391800-56397800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:56391800-56400600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:56391800-56400600	Weak transcription	NHEK	skin
15	chr12:56392000-56395000	Weak transcription	A549	lung
16	chr12:56392000-56395200	Weak transcription	Fetal Kidney	kidney
17	chr12:56392000-56395200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:56392000-56395200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:56392000-56395400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:56392000-56395400	Weak transcription	Right Ventricle	heart
21	chr12:56392000-56395600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:56392000-56395600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:56392000-56395800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:56392000-56395800	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:56392000-56395800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:56392000-56395800	Weak transcription	Osteobl	bone
27	chr12:56392000-56396000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:56392000-56396000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:56392000-56396000	Weak transcription	Brain Substantia Nigra	brain
30	chr12:56392000-56396000	Weak transcription	Fetal Lung	lung
31	chr12:56392000-56396200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:56392000-56396200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:56392000-56396200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:56392000-56396200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:56392000-56396200	Weak transcription	NH-A	brain
36	chr12:56392000-56396400	Weak transcription	Fetal Brain Female	brain
37	chr12:56392000-56396800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:56392000-56397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:56392000-56397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:56392000-56397600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:56392000-56397600	Weak transcription	HSMM	muscle
42	chr12:56392000-56397800	Weak transcription	HSMMtube	muscle
43	chr12:56392000-56399200	Weak transcription	HUVEC	blood vessel
44	chr12:56392000-56400600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:56392000-56400600	Weak transcription	Fetal Thymus	thymus
46	chr12:56392000-56400600	Weak transcription	Right Atrium	heart
47	chr12:56392000-56400600	Weak transcription	HMEC	breast
48	chr12:56392000-56400800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:56392000-56400800	Weak transcription	GM12878-XiMat	blood
50	chr12:56392200-56395200	Weak transcription	Rectal Mucosa Donor 29	rectum

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