Variant report

Variant	rs6897578
Chromosome Location	chr5:90577880-90577881
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	FOS	chr5:90575730-90578000	MCF10A-Er-Src	breast:	n/a	chr5:90577100-90577110 chr5:90576440-90576451 chr5:90576429-90576440 chr5:90577514-90577522 chr5:90577512-90577523
2	EP300	chr5:90575729-90577893	ECC-1	luminal epithelium:	n/a	chr5:90577251-90577258 chr5:90577430-90577444
3	STAT3	chr5:90575692-90577887	MCF10A-Er-Src	breast:	n/a	n/a
4	E2F4	chr5:90577332-90577975	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:90575062-90578172	U87	brain:	n/a	n/a
6	JUN	chr5:90575634-90577990	K562	blood:	n/a	chr5:90577100-90577110 chr5:90577514-90577522
7	KAP1	chr5:90575842-90578127	HEK293	kidney:	n/a	chr5:90577515-90577524
8	SP1	chr5:90575696-90578280	HCT-116	colon:	n/a	n/a
9	STAT3	chr5:90575693-90577984	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr5:90575778-90577898	MCF10A-Er-Src	breast:	n/a	chr5:90577100-90577110 chr5:90576440-90576451 chr5:90576429-90576440 chr5:90577514-90577522 chr5:90577512-90577523
11	MAFK	chr5:90577300-90577929	IMR90	lung:	n/a	chr5:90577514-90577524
12	POLR2A	chr5:90575606-90578001	U87	brain:	n/a	n/a
13	STAT3	chr5:90575756-90577904	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:90575592-90578001	U87	brain:	n/a	n/a
15	FOS	chr5:90575719-90577964	MCF10A-Er-Src	breast:	n/a	chr5:90577100-90577110 chr5:90576440-90576451 chr5:90576429-90576440 chr5:90577514-90577522 chr5:90577512-90577523
16	POLR2A	chr5:90575339-90578013	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr5:90574979-90578172	U87	brain:	n/a	n/a
18	FOXM1	chr5:90575738-90577914	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:90574749..90579554-chr5:90606387..90610471,6	MCF-7	breast:
2	chr5:90574103..90582351-chr5:90673173..90681609,28	K562	blood:
3	chr5:90574805..90578594-chr5:90673900..90681432,13	MCF-7	breast:
4	chr5:90576418..90578111-chr5:90608143..90610210,2	K562	blood:
5	chr5:90573090..90582351-chr5:90673821..90680716,23	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR98-6	chr5:90575897-90578519	NONHSAT102741

Variant related genes	Relation type
ENSG00000234292	TF binding region
ENSG00000113369	Chromatin interaction
ENSG00000271762	Chromatin interaction
ENSG00000248323	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10038090	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10061355	0.89[ASN][1000 genomes]
rs10462343	0.91[ASN][1000 genomes]
rs10462492	0.89[ASN][1000 genomes]
rs10474346	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10474347	0.91[ASN][1000 genomes]
rs10805873	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12697807	0.91[ASN][1000 genomes]
rs13171635	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1511344	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1511345	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543066	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1858309	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2048451	0.94[ASN][1000 genomes]
rs2048452	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973441	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4019243	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4019302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4364415	0.94[ASN][1000 genomes]
rs4377733	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4424024	0.90[ASN][1000 genomes]
rs4518439	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6859170	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6869552	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6882172	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6885341	0.94[ASN][1000 genomes]
rs6888389	0.93[ASN][1000 genomes]
rs6888674	0.93[ASN][1000 genomes]
rs6889197	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6898622	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7709572	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7719516	0.90[ASN][1000 genomes]
rs7724489	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90576800-90583800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:90577000-90578000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:90577000-90578000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr5:90577000-90578000	Enhancers	NHEK	skin
5	chr5:90577000-90578200	Enhancers	HMEC	breast
6	chr5:90577000-90579200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:90577200-90579000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:90577200-90580200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:90577400-90578000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:90577400-90578000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr5:90577400-90578000	Enhancers	NHLF	lung
12	chr5:90577400-90578200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:90577400-90578200	Enhancers	NH-A	brain
14	chr5:90577400-90578200	Enhancers	Osteobl	bone
15	chr5:90577400-90578400	Enhancers	HUVEC	blood vessel
16	chr5:90577400-90578400	Enhancers	NHDF-Ad	bronchial
17	chr5:90577400-90578600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:90577400-90579000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr5:90577400-90579200	Weak transcription	Stomach Mucosa	stomach
20	chr5:90577400-90580400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr5:90577400-90580400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:90577400-90580800	Enhancers	Hela-S3	cervix
23	chr5:90577400-90581000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:90577600-90578000	Enhancers	A549	lung
25	chr5:90577600-90578200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:90577600-90578600	Weak transcription	Placenta	Placenta
27	chr5:90577600-90579200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:90577600-90579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:90577600-90579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:90577600-90579400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:90577600-90579400	Weak transcription	Small Intestine	intestine
32	chr5:90577600-90579600	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:90577600-90579800	Weak transcription	HSMM	muscle
34	chr5:90577600-90583800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:90577800-90579400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:90577800-90583800	Weak transcription	Placenta Amnion	Placenta Amnion

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