Variant report

Variant	rs35228066
Chromosome Location	chr3:119423032-119423033
allele	C/T
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	MXI1	chr3:119421136-119423363	SK-N-SH	brain:	n/a	n/a
2	FOXA1	chr3:119422767-119423136	HepG2	liver:	n/a	chr3:119422962-119422977
3	FOXA1	chr3:119422688-119423210	HepG2	liver:	n/a	chr3:119422962-119422977
4	FOXA1	chr3:119422791-119423212	HepG2	liver:	n/a	chr3:119422962-119422977
5	FOXA1	chr3:119422828-119423155	T-47D	breast:	n/a	chr3:119422962-119422977
6	FOXA2	chr3:119422810-119423133	HepG2	liver:	n/a	n/a
7	FOXA1	chr3:119422774-119423113	HepG2	liver:	n/a	chr3:119422962-119422977
8	EP300	chr3:119422820-119423085	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119422857..119424567-chr7:75925278..75927867,2	MCF-7	breast:
2	chr3:119393569..119396281-chr3:119421855..119424087,2	MCF-7	breast:

Variant related genes	Relation type
MAATS1	TF binding region
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10934496	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11917710	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082557	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092631	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34205825	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34605021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34845376	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35010368	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35012220	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35141348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35403027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35647314	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35864899	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35918837	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35931410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4234664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4444744	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544652	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687877	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4688028	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67287047	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771837	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778570	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786722	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801778	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71325399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72963166	0.93[AFR][1000 genomes]
rs7612861	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612954	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613408	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615769	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7617287	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617290	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624404	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7644545	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847068	0.96[ASN][1000 genomes]
rs9848716	0.96[ASN][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	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv591391	chr3:119403145-119442572	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35228066	MAATS1	cis	Stomach	GTEx
rs35228066	MAATS1	cis	Skin Sun Exposed Lower leg	GTEx
rs35228066	MAATS1	cis	Thyroid	GTEx
rs35228066	MAATS1	cis	Artery Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119421200-119423200	Active TSS	Brain Anterior Caudate	brain
2	chr3:119421200-119423400	Active TSS	Ovary	ovary
3	chr3:119421400-119423200	Flanking Active TSS	Liver	Liver
4	chr3:119421400-119423200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:119422000-119423200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:119422200-119458200	Weak transcription	Aorta	Aorta
7	chr3:119422600-119423200	Enhancers	A549	lung
8	chr3:119422600-119423800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:119422600-119435600	Weak transcription	Pancreas	Pancrea
10	chr3:119422800-119423200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr3:119422800-119423400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:119422800-119423400	Enhancers	Brain Substantia Nigra	brain
13	chr3:119422800-119440000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:119423000-119423200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:119423000-119423200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:119423000-119423200	Flanking Active TSS	Fetal Kidney	kidney
17	chr3:119423000-119428400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:119423000-119432800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:119423000-119433800	Weak transcription	Fetal Intestine Small	intestine
20	chr3:119423000-119434000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:119423000-119435000	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:119423000-119463000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:119423000-119464400	Weak transcription	Brain Cingulate Gyrus	brain

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