Variant report

Variant	rs13083193
Chromosome Location	chr3:143908177-143908178
allele	G/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	ZNF143	chr3:143908019-143908260	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RNA5SP144	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1020376	0.81[EUR][1000 genomes]
rs10212266	0.81[EUR][1000 genomes]
rs1073549	0.81[EUR][1000 genomes]
rs12695778	0.82[EUR][1000 genomes]
rs13067831	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13086045	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13092307	0.81[EUR][1000 genomes]
rs13098262	0.85[ASN][1000 genomes]
rs13319747	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1503334	0.81[EUR][1000 genomes]
rs1503335	0.82[EUR][1000 genomes]
rs1526568	0.82[EUR][1000 genomes]
rs1550781	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16855109	0.82[EUR][1000 genomes]
rs2375134	0.81[EUR][1000 genomes]
rs34050535	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34055143	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35161383	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35404555	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35752283	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35901756	0.81[EUR][1000 genomes]
rs4431107	0.87[TSI][hapmap]
rs62267310	0.85[ASN][1000 genomes]
rs62269942	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440222	0.80[EUR][1000 genomes]
rs6440224	0.81[EUR][1000 genomes]
rs6440225	0.81[EUR][1000 genomes]
rs6440226	0.81[EUR][1000 genomes]
rs67266003	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611449	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7615096	0.87[TSI][hapmap]
rs7624696	0.81[EUR][1000 genomes]
rs7625689	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628853	0.82[EUR][1000 genomes]
rs7630725	0.81[EUR][1000 genomes]
rs7633971	0.81[EUR][1000 genomes]
rs9854202	0.85[TSI][hapmap]
rs9861939	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1010117	chr3:143750590-144093775	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv536748	chr3:143750590-144093775	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv591925	chr3:143821997-144019763	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1007963	chr3:143836773-144000203	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv536750	chr3:143836773-144000203	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1002032	chr3:143848755-144065468	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv877570	chr3:143853149-144123401	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv591926	chr3:143873901-144058395	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv525190	chr3:143899074-143909347	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13083193	TGM6	trans	cerebellum	SCAN
rs13083193	C3orf58	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143898400-143919000	Weak transcription	Ovary	ovary
2	chr3:143906400-143908600	Enhancers	Dnd41	blood
3	chr3:143906600-143908400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:143906600-143908600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:143907000-143908200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:143907200-143908200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:143907200-143908400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:143907200-143908400	Enhancers	Brain Substantia Nigra	brain
9	chr3:143907400-143908400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:143907600-143908200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:143907800-143908200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:143907800-143908200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:143907800-143908200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:143907800-143908800	Enhancers	Brain Hippocampus Middle	brain
15	chr3:143908000-143908200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:143908000-143908200	Enhancers	HSMM	muscle
17	chr3:143908000-143908200	Enhancers	HSMMtube	muscle
18	chr3:143908000-143908200	Enhancers	NH-A	brain
19	chr3:143908000-143908600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:143908000-143908600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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