Variant report

Variant	rs6874823
Chromosome Location	chr5:17304934-17304935
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	BCL3	chr5:17304298-17305641	A549	lung:	n/a	n/a
2	STAT3	chr5:17304435-17306581	Hela-S3	cervix:	n/a	n/a
3	RAD21	chr5:17304920-17307053	A549	lung:	n/a	n/a
4	MAFK	chr5:17304432-17306956	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:17304398-17306616	MCF10A-Er-Src	breast:	n/a	n/a
6	JUN	chr5:17304368-17306594	Hela-S3	cervix:	n/a	chr5:17306385-17306394
7	FOSL2	chr5:17304157-17307175	A549	lung:	n/a	chr5:17306385-17306394
8	RAD21	chr5:17304447-17306741	Hela-S3	cervix:	n/a	n/a
9	RFX5	chr5:17304413-17306767	Hela-S3	cervix:	n/a	chr5:17305160-17305173 chr5:17306238-17306246
10	PRDM1	chr5:17304507-17306560	Hela-S3	cervix:	n/a	chr5:17305658-17305667
11	JUND	chr5:17304390-17306626	Hela-S3	cervix:	n/a	chr5:17304610-17304621 chr5:17306385-17306394
12	GATA3	chr5:17304198-17307181	A549	lung:	n/a	chr5:17305666-17305673
13	EP300	chr5:17304020-17307111	A549	lung:	n/a	chr5:17306172-17306182 chr5:17305961-17305975
14	CEBPB	chr5:17304353-17306743	Hela-S3	cervix:	n/a	chr5:17305113-17305124 chr5:17305113-17305124 chr5:17305305-17305318
15	REST	chr5:17304824-17306790	A549	lung:	n/a	n/a
16	BCL3	chr5:17304497-17306914	A549	lung:	n/a	n/a
17	ATF3	chr5:17304934-17305682	A549	lung:	n/a	n/a
18	TCF12	chr5:17304862-17307035	MCF-7	breast:	n/a	n/a
19	KAP1	chr5:17304232-17305558	U2OS	brain:	n/a	n/a
20	CEBPB	chr5:17304876-17306892	A549	lung:	n/a	chr5:17305113-17305124 chr5:17305113-17305124 chr5:17305305-17305318
21	SP1	chr5:17304159-17307139	A549	lung:	n/a	chr5:17306385-17306397 chr5:17306386-17306395 chr5:17306382-17306396
22	MXI1	chr5:17304281-17306747	Hela-S3	cervix:	n/a	n/a
23	EP300	chr5:17304119-17307097	A549	lung:	n/a	chr5:17306172-17306182 chr5:17305961-17305975
24	MAX	chr5:17304181-17305711	A549	lung:	n/a	n/a
25	RCOR1	chr5:17304393-17306998	Hela-S3	cervix:	n/a	n/a
26	SIN3AK20	chr5:17304911-17307028	MCF-7	breast:	n/a	n/a
27	GABPA	chr5:17304907-17305595	A549	lung:	n/a	n/a
28	BRCA1	chr5:17304511-17306729	Hela-S3	cervix:	n/a	n/a
29	EP300	chr5:17304383-17306612	Hela-S3	cervix:	n/a	chr5:17306172-17306182 chr5:17305961-17305975
30	TBP	chr5:17304401-17306618	Hela-S3	cervix:	n/a	n/a
31	GTF3C2	chr5:17304030-17306399	Hela-S3	cervix:	n/a	n/a
32	GATA3	chr5:17304934-17306996	A549	lung:	n/a	chr5:17305666-17305673
33	SP1	chr5:17304164-17307162	A549	lung:	n/a	chr5:17306385-17306397 chr5:17306386-17306395 chr5:17306382-17306396
34	TCF12	chr5:17304127-17307157	A549	lung:	n/a	n/a
35	SIX5	chr5:17304722-17306997	A549	lung:	n/a	chr5:17304957-17304966

No.	Distal block	Cell Line	Cell type
1	chr5:17223288..17225551-chr5:17303206..17305533,2	MCF-7	breast:
2	chr5:17215446..17220855-chr5:17303141..17309835,13	MCF-7	breast:
3	chr5:16934773..16937451-chr5:17304289..17306411,2	MCF-7	breast:
4	chr5:17215544..17223113-chr5:17298591..17308160,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185296	TF binding region
ENSG00000145555	Chromatin interaction
ENSG00000215196	Chromatin interaction
ENSG00000176788	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10075136	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11949223	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11949279	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869688	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869690	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869693	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134242	0.90[JPT][hapmap]
rs2173968	0.91[JPT][hapmap]
rs2650923	0.90[JPT][hapmap]
rs2650943	0.90[JPT][hapmap]
rs2650944	0.90[JPT][hapmap]
rs2650945	0.90[JPT][hapmap]
rs2652643	0.88[JPT][hapmap]
rs2652645	0.90[JPT][hapmap]
rs2652647	0.91[JPT][hapmap]
rs28665339	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298558	0.90[JPT][hapmap]
rs298560	0.90[JPT][hapmap]
rs60344534	0.83[ASN][1000 genomes]
rs73052845	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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
3	nsv515766	chr5:17283367-17306790	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17296600-17306600	Weak transcription	Aorta	Aorta
2	chr5:17299400-17306600	Weak transcription	Gastric	stomach
3	chr5:17300200-17305400	Weak transcription	Stomach Mucosa	stomach
4	chr5:17301000-17306200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:17301800-17305000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:17302000-17307000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:17302200-17305400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:17302400-17306400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:17302600-17306200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:17302600-17306400	Weak transcription	Ovary	ovary
11	chr5:17302800-17305800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:17302800-17305800	Weak transcription	NHEK	skin
13	chr5:17303000-17305800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:17303000-17306200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:17303000-17306400	Weak transcription	Esophagus	oesophagus
16	chr5:17303600-17305000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr5:17303600-17305200	Weak transcription	Placenta	Placenta
18	chr5:17304000-17306400	Enhancers	Osteobl	bone
19	chr5:17304000-17306800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:17304200-17306200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:17304200-17306800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:17304200-17306800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:17304200-17307000	Flanking Active TSS	Hela-S3	cervix
24	chr5:17304400-17305400	Enhancers	Adipose Nuclei	Adipose
25	chr5:17304400-17305800	Flanking Active TSS	A549	lung
26	chr5:17304400-17307000	Enhancers	NH-A	brain
27	chr5:17304600-17305400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:17304600-17306200	Enhancers	NHLF	lung
29	chr5:17304800-17305000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:17304800-17306000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr5:17304800-17306200	Weak transcription	HSMM	muscle

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