Variant report

Variant	rs62384876
Chromosome Location	chr6:4488560-4488561
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	CBX3	chr6:4488398-4489131	HCT-116	colon:	n/a	n/a
2	CBX3	chr6:4488530-4489100	HCT-116	colon:	n/a	n/a
3	FOSL1	chr6:4487616-4488658	HCT-116	colon:	n/a	chr6:4488565-4488572
4	SETDB1	chr6:4488049-4489394	U2OS	brain:	n/a	n/a
5	TCF12	chr6:4488507-4489220	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4488176..4491651-chr6:4775983..4779929,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260239	TF binding region
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1009602	0.86[ASN][1000 genomes]
rs1009603	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1009604	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1011087	0.81[ASN][1000 genomes]
rs1011088	0.81[ASN][1000 genomes]
rs1011089	0.81[ASN][1000 genomes]
rs1265245	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1265250	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1265256	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1265259	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13195445	0.81[ASN][1000 genomes]
rs1571630	0.81[ASN][1000 genomes]
rs2150231	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3929704	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959295	0.81[ASN][1000 genomes]
rs4959296	0.81[ASN][1000 genomes]
rs4959297	0.81[ASN][1000 genomes]
rs4959299	0.91[ASN][1000 genomes]
rs4959989	0.81[ASN][1000 genomes]
rs4959990	0.81[ASN][1000 genomes]
rs4959991	0.81[ASN][1000 genomes]
rs4959992	0.81[ASN][1000 genomes]
rs4959994	0.81[ASN][1000 genomes]
rs4959995	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959997	0.96[ASN][1000 genomes]
rs4959998	0.84[ASN][1000 genomes]
rs6914063	0.81[ASN][1000 genomes]
rs9378883	0.89[ASN][1000 genomes]
rs9392053	0.81[ASN][1000 genomes]
rs9405748	0.81[ASN][1000 genomes]
rs9502189	0.81[ASN][1000 genomes]
rs9504123	0.81[ASN][1000 genomes]
rs9504124	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv970369	chr6:4481968-4554947	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4487800-4489000	ZNF genes & repeats	Placenta	Placenta
2	chr6:4487800-4489400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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