Variant report

Variant	rs16871757
Chromosome Location	chr5:70746545-70746546
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	chr5:70746081-70746882	SK-N-MC	brain:	n/a	n/a
2	CTCF	chr5:70746400-70746550	SK-N-SH_RA	brain:	n/a	n/a
3	MXI1	chr5:70745941-70747206	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:70746110-70747024	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000250387	TF binding region
BDP1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10038709	0.85[ASN][1000 genomes]
rs10057258	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10079014	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1017225	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942288	0.85[EUR][1000 genomes]
rs10942548	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11739723	0.80[ASN][1000 genomes]
rs12187886	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12652916	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13169095	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13182226	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13183892	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156756	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1990996	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2059196	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs276589	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs277941	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277946	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277947	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs279289	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761966	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs388918	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs411050	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs421128	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs457889	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs458829	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4602607	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs461942	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs462534	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs464639	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs467880	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs467883	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs468010	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468796	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4703987	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4704050	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55884527	0.81[ASN][1000 genomes]
rs561139	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs617876	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67735897	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6872978	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7443752	0.82[ASN][1000 genomes]
rs875136	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9885334	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv528571	chr5:70679626-70767269	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70746200-70746600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
2	chr5:70746200-70746600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:70746200-70746600	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr5:70746200-70746800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:70746200-70747200	Bivalent Enhancer	Fetal Brain Male	brain
6	chr5:70746400-70746600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:70746400-70746600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr5:70746400-70746600	Bivalent Enhancer	Placenta	Placenta
9	chr5:70746400-70746800	Bivalent/Poised TSS	Brain Angular Gyrus	brain

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