Variant report

Variant	rs4959995
Chromosome Location	chr6:4487869-4487870
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	FOS	chr6:4487785-4488241	MCF10A-Er-Src	breast:	n/a	n/a
2	ATF3	chr6:4487812-4488213	HCT-116	colon:	n/a	n/a
3	JUND	chr6:4487850-4488128	K562	blood:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
4	TCF12	chr6:4487839-4488254	ECC-1	luminal epithelium:	n/a	n/a
5	JUND	chr6:4487866-4488058	HepG2	liver:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
6	BACH1	chr6:4487858-4488185	H1-hESC	embryonic stem cell:	n/a	n/a
7	USF1	chr6:4487809-4488187	H1-hESC	embryonic stem cell:	n/a	chr6:4487990-4488001 chr6:4487961-4487972
8	FOSL2	chr6:4487772-4488228	HepG2	liver:	n/a	chr6:4488006-4488017 chr6:4488026-4488037 chr6:4487977-4487988
9	JUND	chr6:4487853-4488053	H1-hESC	embryonic stem cell:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
10	FOSL1	chr6:4487616-4488658	HCT-116	colon:	n/a	chr6:4488565-4488572
11	JUN	chr6:4487852-4488142	K562	blood:	n/a	n/a
12	USF1	chr6:4487821-4488072	H1-hESC	embryonic stem cell:	n/a	chr6:4487990-4488001 chr6:4487961-4487972
13	JUND	chr6:4487832-4488136	HepG2	liver:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
14	EP300	chr6:4487756-4488138	HepG2	liver:	n/a	n/a
15	FOSL1	chr6:4487657-4488275	HCT-116	colon:	n/a	n/a
16	JUND	chr6:4487610-4488296	HCT-116	colon:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
17	FOS	chr6:4487850-4488195	MCF10A-Er-Src	breast:	n/a	n/a
18	JUN	chr6:4487851-4488193	Hela-S3	cervix:	n/a	n/a
19	USF1	chr6:4487869-4488114	ECC-1	luminal epithelium:	n/a	chr6:4487990-4488001 chr6:4487961-4487972
20	FOS	chr6:4487837-4488202	MCF10A-Er-Src	breast:	n/a	n/a
21	JUND	chr6:4487613-4488321	HCT-116	colon:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
22	FOS	chr6:4487859-4488144	MCF10A-Er-Src	breast:	n/a	n/a
23	SRF	chr6:4487801-4488340	HCT-116	colon:	n/a	n/a
24	CEBPB	chr6:4487818-4488219	HCT-116	colon:	n/a	n/a
25	JUND	chr6:4487845-4488194	Hela-S3	cervix:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
26	SRF	chr6:4487613-4488354	HCT-116	colon:	n/a	n/a
27	JUN	chr6:4487776-4488213	K562	blood:	n/a	n/a
28	JUND	chr6:4487810-4488169	A549	lung:	n/a	chr6:4487976-4487987 chr6:4488015-4488026
29	FOSL2	chr6:4487808-4488219	HepG2	liver:	n/a	chr6:4488006-4488017 chr6:4488026-4488037 chr6:4487977-4487988
30	GABPA	chr6:4487868-4488119	Hela-S3	cervix:	n/a	n/a
31	EP300	chr6:4487663-4488291	ECC-1	luminal epithelium:	n/a	chr6:4487741-4487750
32	SP1	chr6:4487679-4488375	HCT-116	colon:	n/a	n/a
33	USF2	chr6:4487829-4488144	Hela-S3	cervix:	n/a	chr6:4487961-4487972 chr6:4487990-4488001
34	SP1	chr6:4487623-4488283	HCT-116	colon:	n/a	n/a
35	FOSL2	chr6:4487720-4488255	A549	lung:	n/a	chr6:4488006-4488017 chr6:4488026-4488037 chr6:4487977-4487988
36	USF1	chr6:4487663-4488283	HCT-116	colon:	n/a	chr6:4487990-4488001 chr6:4487961-4487972
37	POLR2A	chr6:4487828-4488138	HCT-116	colon:	n/a	n/a
38	USF1	chr6:4487788-4488119	ECC-1	luminal epithelium:	n/a	chr6:4487990-4488001 chr6:4487961-4487972
39	USF1	chr6:4487659-4488321	HCT-116	colon:	n/a	chr6:4487990-4488001 chr6:4487961-4487972
40	FOSL2	chr6:4487803-4488203	MCF-7	breast:	n/a	chr6:4488006-4488017 chr6:4488026-4488037 chr6:4487977-4487988
41	CBX3	chr6:4487668-4488356	HCT-116	colon:	n/a	n/a
42	STAT3	chr6:4487722-4488041	MCF10A-Er-Src	breast:	n/a	chr6:4487740-4487748

Variant related genes	Relation type
ENSG00000260239	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009602	0.86[ASN][1000 genomes]
rs1009603	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1009604	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1011087	0.81[ASN][1000 genomes]
rs1011088	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs1011089	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs1265245	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1265250	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1265256	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1265259	0.81[ASN][1000 genomes]
rs13195445	0.81[ASN][1000 genomes]
rs1571630	0.81[ASN][1000 genomes]
rs2150231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3929704	0.97[AMR][1000 genomes];0.96[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]
rs4959993	0.92[CHB][hapmap]
rs4959994	0.81[ASN][1000 genomes]
rs4959997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4959998	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs62384876	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914063	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs878780	0.86[AMR][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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4487600-4488400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:4487800-4489000	ZNF genes & repeats	Placenta	Placenta
3	chr6:4487800-4489400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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