Variant report

Variant	rs55690508
Chromosome Location	chr3:118960049-118960050
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	POLR2A	chr3:118959371-118960111	U87	brain:	n/a	n/a
2	POLR2A	chr3:118958863-118960066	GM12878	blood:	n/a	n/a
3	MAX	chr3:118959647-118960079	A549	lung:	n/a	n/a
4	POLR2A	chr3:118959265-118960069	HUVEC	blood vessel:	n/a	n/a
5	JUND	chr3:118959171-118960049	A549	lung:	n/a	chr3:118959584-118959593
6	NR2F2	chr3:118958898-118960124	MCF-7	breast:	n/a	chr3:118959217-118959232
7	POLR2A	chr3:118959311-118960142	U87	brain:	n/a	n/a
8	RCOR1	chr3:118959631-118960125	GM12878	blood:	n/a	n/a
9	ARID3A	chr3:118959577-118960661	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr3:118958869-118960237	MCF-7	breast:	n/a	n/a
11	MTA3	chr3:118958771-118960073	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:118958207-118960535	MCF10A-Er-Src	breast:	n/a	n/a
13	REST	chr3:118958774-118960761	A549	lung:	n/a	n/a
14	MYC	chr3:118958908-118960675	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:118959398-118960125	SK-N-SH	brain:	n/a	n/a
16	MYC	chr3:118959358-118960065	K562	blood:	n/a	n/a
17	ZNF143	chr3:118959284-118960109	H1-hESC	embryonic stem cell:	n/a	chr3:118959674-118959684 chr3:118959658-118959676 chr3:118959886-118959896 chr3:118959668-118959678
18	POLR2A	chr3:118959129-118960058	HCT-116	colon:	n/a	n/a
19	MAX	chr3:118959117-118960164	A549	lung:	n/a	n/a
20	MAX	chr3:118959643-118960177	MCF-7	breast:	n/a	n/a
21	MAX	chr3:118959331-118960144	MCF-7	breast:	n/a	n/a
22	MXI1	chr3:118959376-118960686	GM12878	blood:	n/a	n/a
23	MAX	chr3:118958795-118960787	A549	lung:	n/a	n/a
24	CTCF	chr3:118959920-118960070	HMF	breast:	n/a	n/a
25	MAX	chr3:118959041-118960696	NB4	blood:	n/a	n/a
26	MAX	chr3:118959238-118960139	ECC-1	luminal epithelium:	n/a	n/a
27	TEAD4	chr3:118959612-118960155	ECC-1	luminal epithelium:	n/a	n/a
28	EGR1	chr3:118959636-118960100	ECC-1	luminal epithelium:	n/a	chr3:118959859-118959873 chr3:118959863-118959872 chr3:118959861-118959876
29	POLR2A	chr3:118959194-118960160	PANC-1	pancreas:	n/a	n/a
30	HEY1	chr3:118958860-118960099	HepG2	liver:	n/a	chr3:118959669-118959684 chr3:118959765-118959780 chr3:118959611-118959626
31	E2F6	chr3:118959426-118960331	A549	lung:	n/a	chr3:118959770-118959780 chr3:118959869-118959876 chr3:118959866-118959877 chr3:118959867-118959877 chr3:118959868-118959876 chr3:118959868-118959876
32	FOSL2	chr3:118959529-118960110	A549	lung:	n/a	chr3:118959584-118959593
33	POLR2A	chr3:118959208-118960077	HUVEC	blood vessel:	n/a	n/a
34	MAX	chr3:118958980-118960056	K562	blood:	n/a	n/a
35	CTCF	chr3:118960011-118960773	HCT-116	colon:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
36	E2F6	chr3:118959296-118960130	H1-hESC	embryonic stem cell:	n/a	chr3:118959770-118959780 chr3:118959869-118959876 chr3:118959866-118959877 chr3:118959867-118959877 chr3:118959868-118959876 chr3:118959868-118959876
37	POLR2A	chr3:118959507-118960060	HL-60	blood:	n/a	n/a
38	POLR2A	chr3:118959305-118960142	U87	brain:	n/a	n/a
39	POLR2A	chr3:118959217-118960080	GM15510	blood:	n/a	n/a
40	RFX5	chr3:118959987-118960331	K562	blood:	n/a	n/a
41	ZNF143	chr3:118959607-118960651	Hela-S3	cervix:	n/a	chr3:118959674-118959684 chr3:118959658-118959676 chr3:118959886-118959896 chr3:118959668-118959678
42	JUND	chr3:118958901-118960061	K562	blood:	n/a	chr3:118959584-118959593
43	BHLHE40	chr3:118959469-118960099	HepG2	liver:	n/a	n/a
44	E2F6	chr3:118959582-118960153	A549	lung:	n/a	chr3:118959770-118959780 chr3:118959869-118959876 chr3:118959866-118959877 chr3:118959867-118959877 chr3:118959868-118959876 chr3:118959868-118959876
45	POLR2A	chr3:118959031-118960628	GM12878	blood:	n/a	n/a
46	EGR1	chr3:118959396-118960634	HCT-116	colon:	n/a	chr3:118959859-118959873 chr3:118959863-118959872 chr3:118959861-118959876
47	GATA3	chr3:118958800-118960067	A549	lung:	n/a	n/a
48	E2F4	chr3:118959312-118960654	MCF10A-Er-Src	breast:	n/a	chr3:118959770-118959780 chr3:118959869-118959876 chr3:118959866-118959877 chr3:118959867-118959877 chr3:118959868-118959876 chr3:118959868-118959876
49	E2F6	chr3:118959400-118960689	H1-hESC	embryonic stem cell:	n/a	chr3:118959770-118959780 chr3:118959869-118959876 chr3:118959866-118959877 chr3:118959867-118959877 chr3:118959868-118959876 chr3:118959868-118959876
50	RCOR1	chr3:118958973-118960146	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:118864340..118865141-chr3:118960015..118960938,2	MCF-7	breast:
2	chr3:118865607..118868236-chr3:118959699..118961355,2	K562	blood:
3	chr3:118944759..118947412-chr3:118958236..118960502,3	MCF-7	breast:
4	chr3:118948357..118951865-chr3:118958522..118961643,4	MCF-7	breast:
5	chr3:118863527..118866220-chr3:118958408..118962544,4	MCF-7	breast:
6	chr13:22177969..22178555-chr3:118959359..118960057,2	NB4	blood:
7	chr3:118863219..118864917-chr3:118959824..118960983,11	MCF-7	breast:
8	chr3:118948409..118952425-chr3:118955700..118962526,10	K562	blood:
9	chr3:118943120..118945710-chr3:118958108..118960423,2	K562	blood:
10	chr17:17739891..17740473-chr3:118959481..118960131,2	HCT-116	colon:
11	chr3:118954516..118958209-chr3:118958247..118961418,8	MCF-7	breast:

Variant related genes	Relation type
B4GALT4	TF binding region
ENSG00000144847	Chromatin interaction
ENSG00000251012	Chromatin interaction
ENSG00000163424	Chromatin interaction
ENSG00000165487	Chromatin interaction
ENSG00000240254	Chromatin interaction
ENSG00000072310	Chromatin interaction
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1584399	0.90[ASN][1000 genomes]
rs67647625	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73187823	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73187824	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73187825	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73187827	0.96[EUR][1000 genomes];0.93[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3405597	chr3:118958287-118960835	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118957200-118960200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:118957400-118960200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:118957400-118960200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:118957400-118960200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:118957400-118960200	Active TSS	NHDF-Ad	bronchial
6	chr3:118957600-118960200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:118957600-118960200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:118957600-118960200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr3:118957600-118960200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:118957600-118960200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr3:118957600-118960200	Active TSS	Right Atrium	heart
12	chr3:118957600-118960400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr3:118957800-118960200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:118958000-118960200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:118958000-118960200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:118958200-118960200	Active TSS	NHLF	lung
17	chr3:118958400-118960200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:118958400-118960400	Active TSS	HepG2	liver
19	chr3:118958600-118960200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:118958600-118960200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr3:118958600-118960200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:118958600-118960200	Active TSS	Brain Substantia Nigra	brain
23	chr3:118958600-118960200	Active TSS	Fetal Muscle Trunk	muscle
24	chr3:118958600-118960200	Active TSS	Psoas Muscle	Psoas
25	chr3:118958600-118960400	Active TSS	Brain Anterior Caudate	brain
26	chr3:118958800-118960200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:118958800-118960200	Active TSS	Primary T cells from cord blood	blood
28	chr3:118958800-118960200	Active TSS	Brain Angular Gyrus	brain
29	chr3:118958800-118960200	Active TSS	Brain Cingulate Gyrus	brain
30	chr3:118959000-118960200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr3:118959000-118960200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:118959000-118960200	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr3:118959200-118960200	Active TSS	Brain Hippocampus Middle	brain
34	chr3:118959200-118960200	Active TSS	Colon Smooth Muscle	Colon
35	chr3:118959200-118960200	Active TSS	Fetal Lung	lung
36	chr3:118959200-118960200	Active TSS	Thymus	Thymus
37	chr3:118959200-118960400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr3:118959200-118960400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:118959200-118960400	Active TSS	Fetal Brain Female	brain
40	chr3:118959200-118960400	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr3:118959200-118960600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:118959400-118960200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:118959400-118960200	Active TSS	Brain Germinal Matrix	brain
44	chr3:118959400-118960200	Active TSS	Hela-S3	cervix
45	chr3:118959800-118960200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:118959800-118960200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:118959800-118960200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr3:118959800-118960200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr3:118959800-118960200	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:118959800-118960200	Flanking Active TSS	Primary B cells from peripheral blood	blood

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