Variant report

Variant	rs638602
Chromosome Location	chr3:43019200-43019201
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	SETDB1	chr3:43018739-43019354	U2OS	brain:	n/a	n/a
2	STAT3	chr3:43019030-43019230	MCF10A-Er-Src	breast:	n/a	chr3:43019157-43019166 chr3:43019158-43019167 chr3:43019210-43019217
3	STAT3	chr3:43019060-43019313	MCF10A-Er-Src	breast:	n/a	chr3:43019157-43019166 chr3:43019158-43019167 chr3:43019210-43019217
4	FOS	chr3:43019093-43019248	MCF10A-Er-Src	breast:	n/a	chr3:43019158-43019167 chr3:43019158-43019166 chr3:43019159-43019166

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43017736..43019452-chr3:43022263..43024227,2	MCF-7	breast:

Variant related genes	Relation type
FAM198A	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10470680	0.83[EUR][1000 genomes]
rs11129987	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11129988	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1346414	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1346415	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17074894	0.82[EUR][1000 genomes]
rs2288371	0.87[ASN][1000 genomes]
rs2288373	0.87[ASN][1000 genomes]
rs2372270	0.80[EUR][1000 genomes]
rs28378297	0.80[EUR][1000 genomes]
rs3915020	0.82[EUR][1000 genomes]
rs526511	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545023	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs551658	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57113579	0.82[ASN][1000 genomes]
rs57664746	0.82[ASN][1000 genomes]
rs57795561	0.82[ASN][1000 genomes]
rs59789275	0.95[ASN][1000 genomes]
rs60046829	0.95[ASN][1000 genomes]
rs60549782	0.82[ASN][1000 genomes]
rs60607395	0.95[ASN][1000 genomes]
rs60616619	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61004728	0.83[EUR][1000 genomes]
rs61102947	0.95[ASN][1000 genomes]
rs615462	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs619660	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249006	0.83[EUR][1000 genomes]
rs62249007	0.83[EUR][1000 genomes]
rs62249008	0.82[EUR][1000 genomes]
rs62249009	0.83[EUR][1000 genomes]
rs62249011	0.83[EUR][1000 genomes]
rs62249013	0.82[EUR][1000 genomes]
rs649682	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6763762	0.83[EUR][1000 genomes]
rs6773223	0.82[EUR][1000 genomes]
rs6775999	0.83[EUR][1000 genomes]
rs6778645	0.87[ASN][1000 genomes]
rs6798412	0.83[EUR][1000 genomes]
rs6798520	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704895	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72869044	0.82[ASN][1000 genomes]
rs72869047	0.82[ASN][1000 genomes]
rs7617715	0.80[EUR][1000 genomes]
rs7621158	0.95[ASN][1000 genomes]
rs7644923	0.83[EUR][1000 genomes]
rs834183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834325	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs834579	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs834584	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs834699	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311330	0.80[EUR][1000 genomes]
rs9311331	0.83[EUR][1000 genomes]
rs9808932	0.82[EUR][1000 genomes]
rs9833284	0.83[EUR][1000 genomes]
rs9852930	0.82[EUR][1000 genomes]
rs9858270	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42978600-43020400	Weak transcription	Ovary	ovary
2	chr3:43016000-43020000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:43016000-43020400	Weak transcription	Pancreas	Pancrea
4	chr3:43016200-43020000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:43016200-43020000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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