Variant report

Variant	rs5744099
Chromosome Location	chr1:223316840-223316841
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	POLR2A	chr1:223316068-223317528	K562	blood:	n/a	n/a
2	ETS1	chr1:223316139-223316909	K562	blood:	n/a	chr1:223316620-223316629 chr1:223316234-223316248
3	POLR2A	chr1:223316110-223317543	K562	blood:	n/a	n/a
4	ARID3A	chr1:223316397-223317000	K562	blood:	n/a	n/a
5	TAL1	chr1:223316528-223317542	K562	blood:	n/a	n/a
6	EP300	chr1:223316181-223316910	K562	blood:	n/a	chr1:223316519-223316535
7	ZMIZ1	chr1:223316141-223316847	K562	blood:	n/a	n/a
8	MAZ	chr1:223315756-223317534	K562	blood:	n/a	chr1:223316630-223316640
9	EP300	chr1:223316628-223317614	GM12878	blood:	n/a	chr1:223317117-223317131
10	E2F6	chr1:223315846-223316860	K562	blood:	n/a	n/a
11	POLR2A	chr1:223316319-223316877	ECC-1	luminal epithelium:	n/a	n/a
12	E2F4	chr1:223316005-223316889	MCF10A-Er-Src	breast:	n/a	n/a
13	RUNX3	chr1:223316514-223316842	GM12878	blood:	n/a	n/a
14	MAZ	chr1:223316084-223317968	GM12878	blood:	n/a	chr1:223316630-223316640
15	POLR2A	chr1:223316237-223316938	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr1:223316036-223317563	K562	blood:	n/a	chr1:223316630-223316640
17	MTA3	chr1:223316624-223317508	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:223316120-223316948	K562	blood:	n/a	n/a
19	TBL1XR1	chr1:223316256-223317497	K562	blood:	n/a	n/a
20	POLR2A	chr1:223316455-223316893	A549	lung:	n/a	n/a
21	POLR2A	chr1:223316045-223317035	SK-N-MC	brain:	n/a	n/a
22	RFX5	chr1:223316271-223317424	GM12878	blood:	n/a	n/a
23	MAX	chr1:223315978-223316931	MCF-7	breast:	n/a	chr1:223316630-223316640
24	ELF1	chr1:223316212-223316855	K562	blood:	n/a	n/a
25	MAX	chr1:223315843-223317614	GM12878	blood:	n/a	chr1:223316630-223316640
26	BACH1	chr1:223316182-223317057	H1-hESC	embryonic stem cell:	n/a	n/a
27	STAT1	chr1:223316562-223317631	GM12878	blood:	n/a	n/a
28	TAF1	chr1:223316377-223316872	K562	blood:	n/a	n/a
29	POLR2A	chr1:223316292-223316924	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr1:223316168-223316955	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr1:223316392-223316883	GM12878	blood:	n/a	n/a
32	ZNF143	chr1:223316191-223317574	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:223315837-223317506	K562	blood:	n/a	n/a
34	RCOR1	chr1:223316311-223316848	Hela-S3	cervix:	n/a	n/a
35	TBL1XR1	chr1:223316722-223317508	K562	blood:	n/a	n/a
36	POLR2A	chr1:223315622-223317565	K562	blood:	n/a	n/a
37	TEAD4	chr1:223315902-223317619	K562	blood:	n/a	chr1:223316981-223316990
38	POLR2A	chr1:223316261-223317074	NB4	blood:	n/a	n/a
39	E2F6	chr1:223315984-223316874	A549	lung:	n/a	n/a
40	BACH1	chr1:223316714-223316893	K562	blood:	n/a	n/a
41	POLR2A	chr1:223316265-223316970	HCT-116	colon:	n/a	n/a
42	POLR2A	chr1:223316201-223317550	K562	blood:	n/a	n/a
43	IRF1	chr1:223316213-223316893	K562	blood:	n/a	chr1:223316469-223316483 chr1:223316627-223316641 chr1:223316661-223316675
44	RUNX3	chr1:223316720-223317491	GM12878	blood:	n/a	n/a
45	PML	chr1:223316122-223317467	K562	blood:	n/a	n/a
46	ZNF263	chr1:223315505-223317578	HEK293-T-REx	kidney:	n/a	chr1:223316428-223316437 chr1:223316429-223316450
47	MAX	chr1:223315959-223317007	ECC-1	luminal epithelium:	n/a	chr1:223316630-223316640
48	POLR2A	chr1:223316446-223316978	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:223316566-223316955	K562	blood:	n/a	n/a
50	CTCF	chr1:223315898-223316878	HCT-116	colon:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470

No.	Distal block	Cell Line	Cell type
1	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:
2	chr1:223306168..223308719-chr1:223316086..223318176,3	MCF-7	breast:
3	chr1:223316576..223317123-chr11:8704194..8704831,2	NB4	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DISP1-3	chr1:223316723-223316940	XLOC_000578

Variant related genes	Relation type
ENSG00000236846	TF binding region
TLR5	TF binding region
ENSG00000166441	Chromatin interaction
ENSG00000187554	Chromatin interaction

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

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

rs_ID	r²[population]
rs2609374	1.00[AMR][1000 genomes]
rs2609375	1.00[AMR][1000 genomes]
rs2609376	1.00[AMR][1000 genomes]
rs5744090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs864310	1.00[AMR][1000 genomes]
rs988781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223315200-223317400	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr1:223315200-223317600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:223315200-223318800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:223315400-223318000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:223315600-223317000	Flanking Active TSS	Fetal Muscle Leg	muscle
6	chr1:223315600-223317200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
7	chr1:223315600-223317200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr1:223315600-223317600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr1:223315800-223317000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:223315800-223317000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:223315800-223317000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:223315800-223317000	Flanking Active TSS	Dnd41	blood
13	chr1:223315800-223317200	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr1:223316000-223317000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr1:223316000-223317000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:223316000-223317000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:223316000-223317000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
18	chr1:223316000-223317000	Flanking Active TSS	Fetal Intestine Large	intestine
19	chr1:223316000-223317000	Flanking Active TSS	Fetal Thymus	thymus
20	chr1:223316000-223317200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:223316000-223317200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr1:223316000-223317200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr1:223316000-223317200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:223316000-223317200	Active TSS	Ovary	ovary
25	chr1:223316000-223318200	Enhancers	Fetal Brain Male	brain
26	chr1:223316200-223317000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:223316200-223317000	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr1:223316200-223317000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:223316200-223317000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:223316200-223317000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:223316200-223317400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:223316400-223317000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:223316400-223317000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:223316400-223317200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:223316400-223317600	Flanking Active TSS	GM12878-XiMat	blood
36	chr1:223316400-223318200	Enhancers	Stomach Mucosa	stomach
37	chr1:223316600-223317000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:223316600-223317000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:223316600-223317000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:223316600-223317000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr1:223316600-223317000	Flanking Active TSS	Esophagus	oesophagus
42	chr1:223316600-223317000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr1:223316600-223317000	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr1:223316600-223317000	Flanking Active TSS	NHLF	lung
45	chr1:223316600-223317200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr1:223316600-223317200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr1:223316600-223317200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:223316600-223317200	Flanking Active TSS	Fetal Brain Female	brain
49	chr1:223316600-223317200	Flanking Active TSS	HSMM	muscle
50	chr1:223316600-223317400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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