Variant report

Variant	rs298558
Chromosome Location	chr5:17341276-17341277
allele	A/C
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	GATA3	chr5:17340919-17341363	MCF-7	breast:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
3	JUND	chr5:17340208-17341372	Hela-S3	cervix:	n/a	chr5:17340643-17340652 chr5:17340509-17340520 chr5:17340642-17340653 chr5:17340645-17340652
4	ELK4	chr5:17341101-17341325	Hela-S3	cervix:	n/a	n/a
5	TCF12	chr5:17340718-17341578	A549	lung:	n/a	n/a
6	USF2	chr5:17340647-17341395	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr5:17340838-17341436	MCF-7	breast:	n/a	n/a
8	TEAD4	chr5:17340883-17341369	MCF-7	breast:	n/a	n/a
9	GTF2F1	chr5:17340077-17341809	Hela-S3	cervix:	n/a	n/a
10	BRCA1	chr5:17340602-17341436	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr5:17340883-17341682	Hela-S3	cervix:	n/a	n/a
12	EP300	chr5:17340716-17341448	Hela-S3	cervix:	n/a	n/a
13	EP300	chr5:17340835-17341409	A549	lung:	n/a	n/a
14	NR2F2	chr5:17340739-17341484	MCF-7	breast:	n/a	n/a
15	KAP1	chr5:17340830-17341370	U2OS	brain:	n/a	n/a
16	TCF7L2	chr5:17340368-17341474	Hela-S3	cervix:	n/a	chr5:17340643-17340652
17	FOXA2	chr5:17340960-17341410	A549	lung:	n/a	chr5:17341112-17341124
18	STAT3	chr5:17340828-17341411	Hela-S3	cervix:	n/a	chr5:17341263-17341277
19	ELF1	chr5:17340898-17341431	MCF-7	breast:	n/a	n/a
20	HDAC2	chr5:17340876-17341379	MCF-7	breast:	n/a	chr5:17341101-17341110 chr5:17340986-17341000 chr5:17340981-17340995
21	EP300	chr5:17340852-17341338	MCF-7	breast:	n/a	n/a
22	MAX	chr5:17340898-17341492	MCF-7	breast:	n/a	n/a
23	SP1	chr5:17340794-17341314	A549	lung:	n/a	n/a
24	FOSL2	chr5:17340454-17341321	A549	lung:	n/a	chr5:17340643-17340652 chr5:17340509-17340520 chr5:17340642-17340653 chr5:17340645-17340652
25	NFYA	chr5:17340893-17341384	Hela-S3	cervix:	n/a	n/a
26	SP1	chr5:17340846-17341437	A549	lung:	n/a	n/a
27	GATA3	chr5:17340545-17341570	A549	lung:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
28	RCOR1	chr5:17340610-17341546	Hela-S3	cervix:	n/a	n/a
29	REST	chr5:17340830-17341368	A549	lung:	n/a	n/a
30	HDAC2	chr5:17340875-17341454	MCF-7	breast:	n/a	chr5:17341101-17341110 chr5:17340986-17341000 chr5:17340981-17340995
31	GATA3	chr5:17340945-17341305	MCF-7	breast:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
32	CHD2	chr5:17340896-17341401	Hela-S3	cervix:	n/a	n/a
33	TCF7L2	chr5:17340966-17341397	MCF-7	breast:	n/a	n/a
34	KAP1	chr5:17340927-17341467	HEK293	kidney:	n/a	n/a
35	NFYB	chr5:17340734-17341453	Hela-S3	cervix:	n/a	chr5:17341137-17341152
36	GATA3	chr5:17340762-17341372	SK-N-SH	brain:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
37	NR2F2	chr5:17340850-17341416	MCF-7	breast:	n/a	n/a
38	RAD21	chr5:17340610-17341434	Hela-S3	cervix:	n/a	n/a
39	PML	chr5:17340997-17341430	MCF-7	breast:	n/a	n/a
40	JUND	chr5:17340760-17341487	MCF-7	breast:	n/a	n/a
41	MYC	chr5:17340583-17341405	Hela-S3	cervix:	n/a	n/a
42	RFX5	chr5:17340640-17341606	Hela-S3	cervix:	n/a	n/a
43	ZNF217	chr5:17340791-17341355	MCF-7	breast:	n/a	n/a
44	GATA3	chr5:17340904-17341414	A549	lung:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
45	MXI1	chr5:17340846-17341462	Hela-S3	cervix:	n/a	chr5:17341385-17341400
46	NFIC	chr5:17340905-17341296	SK-N-SH	brain:	n/a	chr5:17341082-17341098
47	GATA2	chr5:17340945-17341325	HUVEC	blood vessel:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
48	JUN	chr5:17340469-17341368	Hela-S3	cervix:	n/a	chr5:17340643-17340652 chr5:17340509-17340520 chr5:17340642-17340653 chr5:17340645-17340652
49	GATA3	chr5:17340591-17341712	MCF-7	breast:	n/a	chr5:17341099-17341111 chr5:17341102-17341112 chr5:17341081-17341089 chr5:17341102-17341109 chr5:17341100-17341109
50	SMARCC1	chr5:17340169-17341347	Hela-S3	cervix:	n/a	chr5:17340643-17340652

Variant related genes	Relation type
RN7SKP133	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

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]
rs16869688	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs16869690	0.81[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
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	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2173968	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2454946	0.90[EUR][1000 genomes]
rs2459811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap]
rs2650923	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650943	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650944	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];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	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652646	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2652647	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];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]
rs298559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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]
rs6874823	0.90[JPT][hapmap]
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	chr5:17340400-17341400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:17340600-17341400	Enhancers	Stomach Mucosa	stomach
6	chr5:17340600-17341800	Enhancers	Fetal Kidney	kidney
7	chr5:17340600-17343000	Enhancers	Hela-S3	cervix
8	chr5:17340800-17341800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr5:17340800-17343800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:17341000-17341400	Enhancers	HUVEC	blood vessel
11	chr5:17341000-17342000	Enhancers	Aorta	Aorta
12	chr5:17341200-17341400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:17341200-17341600	Enhancers	Fetal Intestine Large	intestine
14	chr5:17341200-17343600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:17341200-17343800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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