Variant report

Variant	rs4959997
Chromosome Location	chr6:4488759-4488760
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	chr6:4488648-4489030	K562	blood:	n/a	n/a
2	CBX3	chr6:4488398-4489131	HCT-116	colon:	n/a	n/a
3	CBX3	chr6:4488530-4489100	HCT-116	colon:	n/a	n/a
4	SETDB1	chr6:4488049-4489394	U2OS	brain:	n/a	n/a
5	CBX3	chr6:4488670-4488959	K562	blood:	n/a	n/a
6	CBX3	chr6:4488601-4489012	K562	blood:	n/a	n/a
7	KAP1	chr6:4488694-4488980	U2OS	brain:	n/a	n/a
8	ZNF143	chr6:4488674-4488875	Hela-S3	cervix:	n/a	n/a
9	KAP1	chr6:4488581-4489147	HEK293	kidney:	n/a	n/a
10	ZNF143	chr6:4488747-4488934	K562	blood:	n/a	n/a
11	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:
2	chr6:4488735..4490606-chr6:4493086..4495998,2	MCF-7	breast:

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

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1009602	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1009603	0.89[ASN][1000 genomes]
rs1009604	0.89[ASN][1000 genomes]
rs1011088	0.92[CHB][hapmap]
rs1011089	0.93[CHB][hapmap]
rs11752793	0.84[AMR][1000 genomes]
rs1265245	0.82[ASN][1000 genomes]
rs1265250	0.88[ASN][1000 genomes]
rs1265256	0.94[ASN][1000 genomes]
rs2021989	0.82[ASN][1000 genomes]
rs2150231	1.00[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs2181015	0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs2875945	0.82[ASN][1000 genomes]
rs3929704	0.95[ASN][1000 genomes]
rs4246070	0.81[ASN][1000 genomes]
rs4959298	0.82[ASN][1000 genomes]
rs4959299	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4959300	0.84[AMR][1000 genomes]
rs4959987	0.80[ASN][1000 genomes]
rs4959993	0.92[CHB][hapmap]
rs4959995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4959998	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57361712	0.84[AMR][1000 genomes]
rs60221507	0.82[ASN][1000 genomes]
rs61449781	0.84[AMR][1000 genomes]
rs62384876	0.96[ASN][1000 genomes]
rs6914063	0.92[CHB][hapmap]
rs7450179	0.81[ASN][1000 genomes]
rs7452972	0.81[ASN][1000 genomes]
rs7453574	0.81[ASN][1000 genomes]
rs911566	0.81[ASN][1000 genomes]
rs911567	0.81[ASN][1000 genomes]
rs9378879	0.81[ASN][1000 genomes]
rs9378880	0.81[ASN][1000 genomes]
rs9378881	0.81[ASN][1000 genomes]
rs9378882	0.82[ASN][1000 genomes]
rs9378883	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9392603	0.81[ASN][1000 genomes]
rs9405247	0.82[ASN][1000 genomes]
rs9405248	0.82[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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