Variant report

Variant	rs9843728
Chromosome Location	chr3:133501407-133501408
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	POLR2A	chr3:133500444-133501555	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:133500242-133502055	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:133500928-133501977	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SRPRB	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12490148	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12595	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079426	0.86[EUR][1000 genomes]
rs1358024	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs1525889	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1830083	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1830084	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1880669	0.86[CHD][hapmap]
rs2692695	0.87[CHD][hapmap]
rs34252038	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34805309	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35332919	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3811647	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811658	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854760	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854761	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854762	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439439	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6762719	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6794945	0.84[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7638018	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8177224	0.87[MEX][hapmap]
rs8177240	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177245	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177247	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177248	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177252	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177253	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177256	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177259	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177260	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177261	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177262	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177271	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8177272	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8177295	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8177297	0.83[ASN][1000 genomes]
rs9813689	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9871148	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9882812	0.82[AMR][1000 genomes];0.83[EUR][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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv4018	chr3:133485867-133530668	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9843728	TOPBP1	cis	parietal	SCAN
rs9843728	SMN1	trans	lymphoblastoid	seeQTL
rs9843728	SRPRB	cis	parietal	SCAN
rs9843728	SMN2	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133497400-133502600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:133498400-133503400	Weak transcription	Adipose Nuclei	Adipose
3	chr3:133498600-133505800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:133498600-133510400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:133498800-133508000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:133499000-133505200	Weak transcription	Brain Anterior Caudate	brain
7	chr3:133499000-133510800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:133499200-133503400	Weak transcription	Brain Substantia Nigra	brain

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