Variant report

Variant	rs299387
Chromosome Location	chr5:17378075-17378076
allele	A/G
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	GTF3C2	chr5:17377755-17378677	Hela-S3	cervix:	n/a	n/a
2	STAT1	chr5:17377840-17380245	Hela-S3	cervix:	n/a	chr5:17378567-17378581
3	JUN	chr5:17378035-17379993	Hela-S3	cervix:	n/a	chr5:17378834-17378842 chr5:17378835-17378846 chr5:17378832-17378844
4	EP300	chr5:17378020-17379156	A549	lung:	n/a	chr5:17378559-17378569
5	RCOR1	chr5:17378003-17379314	IMR90	lung:	n/a	n/a
6	BRCA1	chr5:17377970-17379954	Hela-S3	cervix:	n/a	n/a
7	TCF12	chr5:17377861-17379564	A549	lung:	n/a	n/a
8	MAX	chr5:17378057-17379134	A549	lung:	n/a	n/a
9	KAP1	chr5:17378042-17380078	U2OS	brain:	n/a	n/a
10	JUND	chr5:17378036-17379672	Hela-S3	cervix:	n/a	chr5:17378834-17378842 chr5:17378835-17378846 chr5:17378832-17378844

No.	Distal block	Cell Line	Cell type
1	chr5:17374822..17377145-chr5:17377368..17380212,2	K562	blood:
2	chr5:17374463..17376322-chr5:17377368..17380030,2	K562	blood:
3	chr5:17216760..17218355-chr5:17375692..17378391,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYO10-3	chr5:17378026-17378606	XLOC_004746

Variant related genes	Relation type
ENSG00000249199	TF binding region
ENSG00000249199	Chromatin interaction
ENSG00000176788	Chromatin interaction
ENSG00000215196	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs159605	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs159606	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs177108	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2454947	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2459814	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2459816	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2459825	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2859621	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298540	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72740529	0.93[ASN][1000 genomes]
rs7726183	0.88[ASN][1000 genomes]
rs7736809	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs904861	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
5	esv1793466	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	esv1801170	chr5:17364700-17721569	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	esv1820519	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	esv1824831	chr5:17364700-17721569	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	esv1827359	chr5:17364700-17721569	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	esv1828062	chr5:17364700-17721569	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv427713	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv428464	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	esv2757986	chr5:17364700-17936404	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	esv2759328	chr5:17364700-17936404	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv1017469	chr5:17373383-17416643	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17371200-17378200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:17371400-17378200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:17374400-17378200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:17375600-17378400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:17375600-17380800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:17375800-17378200	Weak transcription	Ovary	ovary
7	chr5:17375800-17378200	Weak transcription	NH-A	brain
8	chr5:17375800-17379200	Weak transcription	HMEC	breast
9	chr5:17375800-17379400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:17375800-17380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:17375800-17380400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:17375800-17380400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:17375800-17380400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:17375800-17380800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:17375800-17387000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:17377800-17378200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:17377800-17378200	Enhancers	A549	lung
18	chr5:17377800-17380000	Enhancers	NHLF	lung
19	chr5:17377800-17382200	Enhancers	Placenta	Placenta
20	chr5:17378000-17378400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:17378000-17379600	Flanking Active TSS	Hela-S3	cervix
22	chr5:17378000-17380000	Enhancers	Fetal Lung	lung
23	chr5:17378000-17381200	Enhancers	Osteobl	bone

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