Variant report

Variant	rs298559
Chromosome Location	chr5:17341414-17341415
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	SIN3AK20	chr5:17340738-17341531	MCF-7	breast:	n/a	n/a
2	TCF12	chr5:17340718-17341578	A549	lung:	n/a	n/a
3	CEBPB	chr5:17340838-17341436	MCF-7	breast:	n/a	n/a
4	GTF2F1	chr5:17340077-17341809	Hela-S3	cervix:	n/a	n/a
5	BRCA1	chr5:17340602-17341436	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr5:17340883-17341682	Hela-S3	cervix:	n/a	n/a
7	EP300	chr5:17340716-17341448	Hela-S3	cervix:	n/a	n/a
8	NR2F2	chr5:17340739-17341484	MCF-7	breast:	n/a	n/a
9	TCF7L2	chr5:17340368-17341474	Hela-S3	cervix:	n/a	chr5:17340643-17340652
10	ELF1	chr5:17340898-17341431	MCF-7	breast:	n/a	n/a
11	MAX	chr5:17340898-17341492	MCF-7	breast:	n/a	n/a
12	SP1	chr5:17340846-17341437	A549	lung:	n/a	n/a
13	GATA3	chr5:17340545-17341570	A549	lung:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
14	RCOR1	chr5:17340610-17341546	Hela-S3	cervix:	n/a	n/a
15	HDAC2	chr5:17340875-17341454	MCF-7	breast:	n/a	chr5:17341101-17341110 chr5:17340986-17341000 chr5:17340981-17340995
16	KAP1	chr5:17340927-17341467	HEK293	kidney:	n/a	n/a
17	NFYB	chr5:17340734-17341453	Hela-S3	cervix:	n/a	chr5:17341137-17341152
18	NR2F2	chr5:17340850-17341416	MCF-7	breast:	n/a	n/a
19	RAD21	chr5:17340610-17341434	Hela-S3	cervix:	n/a	n/a
20	PML	chr5:17340997-17341430	MCF-7	breast:	n/a	n/a
21	JUND	chr5:17340760-17341487	MCF-7	breast:	n/a	n/a
22	RFX5	chr5:17340640-17341606	Hela-S3	cervix:	n/a	n/a
23	GATA3	chr5:17340904-17341414	A549	lung:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
24	MXI1	chr5:17340846-17341462	Hela-S3	cervix:	n/a	chr5:17341385-17341400
25	GATA3	chr5:17340591-17341712	MCF-7	breast:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
26	GATA3	chr5:17340744-17341432	MCF-7	breast:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
27	FOXM1	chr5:17340764-17341463	MCF-7	breast:	n/a	n/a
28	TCF12	chr5:17340930-17341451	MCF-7	breast:	n/a	n/a
29	EP300	chr5:17340707-17341478	A549	lung:	n/a	n/a
30	PRDM1	chr5:17340474-17341481	Hela-S3	cervix:	n/a	chr5:17340643-17340652
31	STAT1	chr5:17339842-17342066	Hela-S3	cervix:	n/a	chr5:17340734-17340742 chr5:17341263-17341277 chr5:17341183-17341194
32	SMC3	chr5:17340740-17341474	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr5:17340683-17341466	MCF-7	breast:	n/a	n/a
34	CEBPB	chr5:17340873-17341425	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RN7SKP133	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10074496	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10462609	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11950287	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13355635	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs182441	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1827400	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2134241	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2134242	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2173968	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2454946	0.90[EUR][1000 genomes]
rs2650923	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650935	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2650936	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650937	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650938	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650939	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650940	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650942	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650943	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650944	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650945	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652638	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2652639	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652640	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2652641	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2652643	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652644	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652645	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652646	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652647	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652648	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28476505	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs298530	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs298531	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs298532	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs298534	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298535	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs298536	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs298546	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298547	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298548	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298550	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298560	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299384	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs299385	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs299386	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56663279	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56705013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58062922	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58468495	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6862515	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052871	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73052881	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73052887	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73052888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73052898	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73052901	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73054809	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054823	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7719794	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17339400-17343800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:17340000-17343600	Enhancers	A549	lung
3	chr5:17340200-17342000	Enhancers	Fetal Lung	lung
4	chr5:17340600-17341800	Enhancers	Fetal Kidney	kidney
5	chr5:17340600-17343000	Enhancers	Hela-S3	cervix
6	chr5:17340800-17341800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr5:17340800-17343800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:17341000-17342000	Enhancers	Aorta	Aorta
9	chr5:17341200-17341600	Enhancers	Fetal Intestine Large	intestine
10	chr5:17341200-17343600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:17341200-17343800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:17341400-17343600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:17341400-17343600	Weak transcription	Stomach Mucosa	stomach
14	chr5:17341400-17343600	Weak transcription	HUVEC	blood vessel
15	chr5:17341400-17343600	Weak transcription	Osteobl	bone

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