Variant report

Variant	rs1473048
Chromosome Location	chr5:90577436-90577437
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	FOXM1	chr5:90576082-90577821	ECC-1	luminal epithelium:	n/a	n/a
2	TCF7L2	chr5:90576037-90577593	HEK293	kidney:	n/a	n/a
3	MAZ	chr5:90575718-90577716	IMR90	lung:	n/a	n/a
4	ZKSCAN1	chr5:90577204-90577662	Hela-S3	cervix:	n/a	n/a
5	NFIC	chr5:90575700-90577871	ECC-1	luminal epithelium:	n/a	n/a
6	RAD21	chr5:90575770-90577621	Hela-S3	cervix:	n/a	n/a
7	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
8	ZMIZ1	chr5:90577397-90577536	K562	blood:	n/a	n/a
9	FOS	chr5:90575842-90577696	MCF10A-Er-Src	breast:	n/a	chr5:90577100-90577110 chr5:90576440-90576451 chr5:90576429-90576440 chr5:90577514-90577522 chr5:90577512-90577523
10	EP300	chr5:90575729-90577893	ECC-1	luminal epithelium:	n/a	chr5:90577251-90577258 chr5:90577430-90577444
11	STAT3	chr5:90575692-90577887	MCF10A-Er-Src	breast:	n/a	n/a
12	E2F4	chr5:90577332-90577975	MCF10A-Er-Src	breast:	n/a	n/a
13	SP1	chr5:90575736-90577843	HCT-116	colon:	n/a	n/a
14	POLR2A	chr5:90575711-90577588	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:90575683-90577641	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr5:90575062-90578172	U87	brain:	n/a	n/a
17	POLR2A	chr5:90575628-90577633	PANC-1	pancreas:	n/a	n/a
18	CCNT2	chr5:90577368-90577577	K562	blood:	n/a	n/a
19	FOSL2	chr5:90575583-90577723	A549	lung:	n/a	chr5:90577100-90577110 chr5:90577514-90577522 chr5:90576428-90576439 chr5:90576441-90576452
20	TCF12	chr5:90575589-90577680	A549	lung:	n/a	chr5:90577364-90577371
21	RCOR1	chr5:90575687-90577545	Hela-S3	cervix:	n/a	n/a
22	NFIC	chr5:90576975-90577740	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr5:90577170-90577701	ECC-1	luminal epithelium:	n/a	n/a
24	JUN	chr5:90575634-90577990	K562	blood:	n/a	chr5:90577100-90577110 chr5:90577514-90577522
25	POLR2A	chr5:90575199-90577599	HUVEC	blood vessel:	n/a	n/a
26	TCF7L2	chr5:90575976-90577544	PANC-1	pancreas:	n/a	n/a
27	ESR1	chr5:90577069-90577704	ECC-1	luminal epithelium:	n/a	n/a
28	SMARCC1	chr5:90575875-90577658	Hela-S3	cervix:	n/a	chr5:90577514-90577523
29	TAF1	chr5:90577218-90577619	Hela-S3	cervix:	n/a	n/a
30	EP300	chr5:90575827-90577717	Hela-S3	cervix:	n/a	chr5:90577251-90577258 chr5:90577430-90577444
31	KAP1	chr5:90575842-90578127	HEK293	kidney:	n/a	chr5:90577515-90577524
32	SP1	chr5:90575696-90578280	HCT-116	colon:	n/a	n/a
33	STAT3	chr5:90575693-90577984	MCF10A-Er-Src	breast:	n/a	n/a
34	JUN	chr5:90575996-90577701	HUVEC	blood vessel:	n/a	chr5:90577100-90577110 chr5:90577514-90577522
35	MYC	chr5:90575734-90577594	MCF10A-Er-Src	breast:	n/a	chr5:90576715-90576725 chr5:90576674-90576684
36	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
37	JUND	chr5:90575737-90577857	HCT-116	colon:	n/a	chr5:90577100-90577110 chr5:90576440-90576451 chr5:90577514-90577522 chr5:90576429-90576440
38	POLR2A	chr5:90577218-90577629	HUVEC	blood vessel:	n/a	n/a
39	JUND	chr5:90575768-90577748	SK-N-SH	brain:	n/a	chr5:90577100-90577110 chr5:90576440-90576451 chr5:90577514-90577522 chr5:90576429-90576440
40	STAT3	chr5:90575715-90577869	MCF10A-Er-Src	breast:	n/a	n/a
41	TCF12	chr5:90575721-90577792	ECC-1	luminal epithelium:	n/a	chr5:90577364-90577371
42	POLR2A	chr5:90577040-90577589	Hela-S3	cervix:	n/a	n/a
43	TEAD4	chr5:90577065-90577715	ECC-1	luminal epithelium:	n/a	n/a
44	ESR1	chr5:90577170-90577516	ECC-1	luminal epithelium:	n/a	n/a
45	STAT1	chr5:90575706-90577599	Hela-S3	cervix:	n/a	chr5:90576523-90576534
46	EP300	chr5:90577045-90577684	ECC-1	luminal epithelium:	n/a	chr5:90577251-90577258 chr5:90577430-90577444
47	TCF12	chr5:90575737-90577698	ECC-1	luminal epithelium:	n/a	chr5:90577364-90577371
48	MAFK	chr5:90577300-90577929	IMR90	lung:	n/a	chr5:90577514-90577524
49	POLR2A	chr5:90575606-90578001	U87	brain:	n/a	n/a
50	SETDB1	chr5:90577086-90577625	U2OS	brain:	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
ENSG00000248323	Chromatin interaction
ENSG00000271762	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2102553	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137010	1.00[CHB][hapmap]
rs2941889	1.00[ASN][1000 genomes]
rs2941903	1.00[ASN][1000 genomes]
rs2973465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2973471	1.00[ASN][1000 genomes]
rs6884883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73179864	1.00[ASN][1000 genomes]
rs867831	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs995691	1.00[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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90575200-90577600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:90576000-90577800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr5:90576600-90577600	Enhancers	Small Intestine	intestine
4	chr5:90576800-90577600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:90576800-90577600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:90576800-90577600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:90576800-90577600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr5:90576800-90577600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:90576800-90577600	Enhancers	Placenta	Placenta
10	chr5:90576800-90577600	Flanking Active TSS	A549	lung
11	chr5:90576800-90583800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:90577000-90577600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:90577000-90577600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:90577000-90577600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:90577000-90577600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:90577000-90577600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:90577000-90577600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:90577000-90577600	Enhancers	Brain Substantia Nigra	brain
19	chr5:90577000-90577600	Enhancers	Colon Smooth Muscle	Colon
20	chr5:90577000-90577600	Enhancers	Rectal Smooth Muscle	rectum
21	chr5:90577000-90577600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr5:90577000-90577600	Enhancers	HSMM	muscle
23	chr5:90577000-90577600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr5:90577000-90577800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
25	chr5:90577000-90578000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:90577000-90578000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr5:90577000-90578000	Enhancers	NHEK	skin
28	chr5:90577000-90578200	Enhancers	HMEC	breast
29	chr5:90577000-90579200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:90577200-90577600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
31	chr5:90577200-90577600	Enhancers	Adipose Nuclei	Adipose
32	chr5:90577200-90577600	Enhancers	Psoas Muscle	Psoas
33	chr5:90577200-90577600	Enhancers	HepG2	liver
34	chr5:90577200-90577600	Enhancers	K562	blood
35	chr5:90577200-90579000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:90577200-90580200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:90577400-90577600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:90577400-90577600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr5:90577400-90577600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr5:90577400-90577600	Enhancers	GM12878-XiMat	blood
41	chr5:90577400-90578000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr5:90577400-90578000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr5:90577400-90578000	Enhancers	NHLF	lung
44	chr5:90577400-90578200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:90577400-90578200	Enhancers	NH-A	brain
46	chr5:90577400-90578200	Enhancers	Osteobl	bone
47	chr5:90577400-90578400	Enhancers	HUVEC	blood vessel
48	chr5:90577400-90578400	Enhancers	NHDF-Ad	bronchial
49	chr5:90577400-90578600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:90577400-90579000	Enhancers	Primary T helper cells PMA-I stimulated	--

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