Variant report

Variant	rs4687842
Chromosome Location	chr3:118960251-118960252
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	ARID3A	chr3:118959577-118960661	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:118958207-118960535	MCF10A-Er-Src	breast:	n/a	n/a
3	REST	chr3:118958774-118960761	A549	lung:	n/a	n/a
4	MYC	chr3:118958908-118960675	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr3:118959376-118960686	GM12878	blood:	n/a	n/a
6	MAX	chr3:118958795-118960787	A549	lung:	n/a	n/a
7	MAX	chr3:118959041-118960696	NB4	blood:	n/a	n/a
8	ATF2	chr3:118960243-118960740	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:118960251-118960456	MCF10A-Er-Src	breast:	n/a	n/a
10	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
11	ELF1	chr3:118960243-118960633	A549	lung:	n/a	n/a
12	SP1	chr3:118960177-118960748	A549	lung:	n/a	n/a
13	CTCF	chr3:118960011-118960773	HCT-116	colon:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
14	RFX5	chr3:118959987-118960331	K562	blood:	n/a	n/a
15	ZNF143	chr3:118959607-118960651	Hela-S3	cervix:	n/a	chr3:118959674-118959684 chr3:118959658-118959676 chr3:118959886-118959896 chr3:118959668-118959678
16	RAD21	chr3:118960162-118960721	ECC-1	luminal epithelium:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
17	POLR2A	chr3:118959031-118960628	GM12878	blood:	n/a	n/a
18	EGR1	chr3:118959396-118960634	HCT-116	colon:	n/a	chr3:118959859-118959873 chr3:118959863-118959872 chr3:118959861-118959876
19	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
20	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
21	CTCF	chr3:118960201-118960698	A549	lung:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
22	NR2F2	chr3:118960213-118960716	MCF-7	breast:	n/a	n/a
23	GATA1	chr3:118958611-118960500	PBDE	blood:	n/a	chr3:118958675-118958692
24	BHLHE40	chr3:118959287-118960685	GM12878	blood:	n/a	n/a
25	USF2	chr3:118960232-118960633	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr3:118960250-118960755	HepG2	liver:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
27	RAD21	chr3:118960219-118960748	MCF-7	breast:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
28	CTCF	chr3:118959143-118960779	SK-N-SH	brain:	n/a	chr3:118959890-118959903 chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
29	CHD1	chr3:118958405-118960749	IMR90	lung:	n/a	chr3:118959806-118959816
30	STAT5A	chr3:118960242-118960620	GM12878	blood:	n/a	n/a
31	MAX	chr3:118958861-118960700	HepG2	liver:	n/a	n/a
32	RAD21	chr3:118960190-118960711	H1-hESC	embryonic stem cell:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
33	POLR2A	chr3:118958262-118960665	HepG2	liver:	n/a	n/a
34	RAD21	chr3:118960205-118960770	MCF-7	breast:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
35	CTCF	chr3:118960188-118960749	K562	blood:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
36	RUNX3	chr3:118960210-118960706	GM12878	blood:	n/a	n/a
37	RAD21	chr3:118960179-118960838	HCT-116	colon:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
38	SIX5	chr3:118959843-118960755	A549	lung:	n/a	n/a
39	MAX	chr3:118959239-118960781	HCT-116	colon:	n/a	n/a
40	RAD21	chr3:118960129-118960778	HCT-116	colon:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
41	IRF1	chr3:118959614-118960578	K562	blood:	n/a	chr3:118959799-118959813
42	HA-E2F1	chr3:118958945-118960667	MCF-7	breast:	n/a	chr3:118959770-118959780 chr3:118959869-118959876 chr3:118959866-118959877 chr3:118959867-118959877 chr3:118959868-118959876 chr3:118959868-118959876
43	CTCF	chr3:118959736-118960723	GM12878	blood:	n/a	chr3:118959890-118959903 chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
44	TCF12	chr3:118958651-118960732	A549	lung:	n/a	n/a
45	RAD21	chr3:118960181-118960749	A549	lung:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
46	RCOR1	chr3:118959138-118960662	Hela-S3	cervix:	n/a	n/a
47	RAD21	chr3:118958647-118960912	SK-N-SH	brain:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517
48	CTCF	chr3:118960239-118960753	MCF-7	breast:	n/a	chr3:118960496-118960517 chr3:118960502-118960518 chr3:118960501-118960519 chr3:118960508-118960515
49	MAX	chr3:118959516-118960636	ECC-1	luminal epithelium:	n/a	n/a
50	RAD21	chr3:118960247-118960732	HepG2	liver:	n/a	chr3:118960499-118960518 chr3:118960508-118960517 chr3:118960503-118960517

No.	Distal block	Cell Line	Cell type
1	chr3:118866560..118867342-chr3:118960209..118960801,2	MCF-7	breast:
2	chr3:118864340..118865141-chr3:118960015..118960938,2	MCF-7	breast:
3	chr3:118865607..118868236-chr3:118959699..118961355,2	K562	blood:
4	chr3:118864376..118864922-chr3:118960063..118960873,2	K562	blood:
5	chr3:118944759..118947412-chr3:118958236..118960502,3	MCF-7	breast:
6	chr3:118948357..118951865-chr3:118958522..118961643,4	MCF-7	breast:
7	chr3:118863527..118866220-chr3:118958408..118962544,4	MCF-7	breast:
8	chr3:118863219..118864917-chr3:118959824..118960983,11	MCF-7	breast:
9	chr3:118948409..118952425-chr3:118955700..118962526,10	K562	blood:
10	chr3:118943120..118945710-chr3:118958108..118960423,2	K562	blood:
11	chr3:118954516..118958209-chr3:118958247..118961418,8	MCF-7	breast:

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

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2717264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687849	1.00[AMR][1000 genomes]
rs4687850	1.00[AMR][1000 genomes]
rs4687999	1.00[AMR][1000 genomes]
rs6438513	0.85[AFR][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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118957600-118960400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr3:118958400-118960400	Active TSS	HepG2	liver
3	chr3:118958600-118960400	Active TSS	Brain Anterior Caudate	brain
4	chr3:118959200-118960400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:118959200-118960400	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr3:118959200-118960400	Active TSS	Fetal Brain Female	brain
7	chr3:118959200-118960400	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr3:118959200-118960600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:118959800-118960400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:118959800-118960400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:118959800-118960400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr3:118959800-118960400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:118959800-118960400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr3:118959800-118960600	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr3:118959800-118960600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr3:118959800-118960600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:118959800-118961200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:118960000-118960400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:118960000-118960400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:118960000-118960400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr3:118960000-118960400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:118960000-118960400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:118960000-118960400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr3:118960000-118960400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr3:118960000-118960400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:118960000-118960400	Enhancers	Fetal Kidney	kidney
27	chr3:118960000-118960400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr3:118960000-118960400	Weak transcription	Spleen	Spleen
29	chr3:118960000-118960400	Flanking Active TSS	GM12878-XiMat	blood
30	chr3:118960000-118960400	Flanking Active TSS	NHEK	skin
31	chr3:118960000-118960600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:118960000-118960600	Enhancers	Fetal Stomach	stomach
33	chr3:118960000-118960600	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr3:118960000-118960600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:118960000-118960800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:118960000-118960800	Enhancers	Liver	Liver
37	chr3:118960000-118960800	Enhancers	Stomach Mucosa	stomach
38	chr3:118960000-118960800	Flanking Active TSS	A549	lung
39	chr3:118960000-118962000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:118960000-118962600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:118960000-118964400	Weak transcription	Esophagus	oesophagus
42	chr3:118960200-118960400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:118960200-118960400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:118960200-118960400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:118960200-118960400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr3:118960200-118960400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:118960200-118960400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr3:118960200-118960400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:118960200-118960400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr3:118960200-118960400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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