Variant report

Variant	rs5744098
Chromosome Location	chr1:223317011-223317012
allele	A/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	POLR2A	chr1:223316110-223317543	K562	blood:	n/a	n/a
3	TAL1	chr1:223316528-223317542	K562	blood:	n/a	n/a
4	MAZ	chr1:223315756-223317534	K562	blood:	n/a	chr1:223316630-223316640
5	EP300	chr1:223316628-223317614	GM12878	blood:	n/a	chr1:223317117-223317131
6	FOXM1	chr1:223317011-223317521	GM12878	blood:	n/a	n/a
7	MAZ	chr1:223316084-223317968	GM12878	blood:	n/a	chr1:223316630-223316640
8	MYC	chr1:223316036-223317563	K562	blood:	n/a	chr1:223316630-223316640
9	MTA3	chr1:223316624-223317508	GM12878	blood:	n/a	n/a
10	TBL1XR1	chr1:223316256-223317497	K562	blood:	n/a	n/a
11	IKZF1	chr1:223316975-223317507	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:223316045-223317035	SK-N-MC	brain:	n/a	n/a
13	RFX5	chr1:223316271-223317424	GM12878	blood:	n/a	n/a
14	MAX	chr1:223315843-223317614	GM12878	blood:	n/a	chr1:223316630-223316640
15	BACH1	chr1:223316182-223317057	H1-hESC	embryonic stem cell:	n/a	n/a
16	STAT1	chr1:223316562-223317631	GM12878	blood:	n/a	n/a
17	ZNF143	chr1:223316191-223317574	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:223315837-223317506	K562	blood:	n/a	n/a
19	MEF2A	chr1:223316995-223317584	K562	blood:	n/a	chr1:223317291-223317306 chr1:223317292-223317306
20	TBL1XR1	chr1:223316722-223317508	K562	blood:	n/a	n/a
21	POLR2A	chr1:223315622-223317565	K562	blood:	n/a	n/a
22	TEAD4	chr1:223315902-223317619	K562	blood:	n/a	chr1:223316981-223316990
23	POLR2A	chr1:223316261-223317074	NB4	blood:	n/a	n/a
24	POLR2A	chr1:223316201-223317550	K562	blood:	n/a	n/a
25	RUNX3	chr1:223316720-223317491	GM12878	blood:	n/a	n/a
26	PML	chr1:223316122-223317467	K562	blood:	n/a	n/a
27	ZNF263	chr1:223315505-223317578	HEK293-T-REx	kidney:	n/a	chr1:223316428-223316437 chr1:223316429-223316450
28	EP300	chr1:223316703-223317780	GM12878	blood:	n/a	chr1:223317117-223317131
29	HA-E2F1	chr1:223316120-223317079	MCF-7	breast:	n/a	n/a
30	E2F6	chr1:223315633-223317591	K562	blood:	n/a	n/a
31	JUND	chr1:223316103-223317013	K562	blood:	n/a	chr1:223316244-223316254 chr1:223316474-223316483
32	NFIC	chr1:223316992-223317548	GM12878	blood:	n/a	n/a
33	CTCF	chr1:223315525-223317318	A549	lung:	n/a	chr1:223316368-223316384 chr1:223315736-223315743 chr1:223316172-223316185 chr1:223316457-223316470
34	KAP1	chr1:223316082-223317105	U2OS	brain:	n/a	n/a
35	NR2F2	chr1:223316138-223317060	K562	blood:	n/a	n/a
36	IRF1	chr1:223316266-223317471	K562	blood:	n/a	chr1:223317159-223317166 chr1:223316469-223316483 chr1:223316627-223316641 chr1:223316661-223316675
37	RCOR1	chr1:223315948-223317737	K562	blood:	n/a	n/a
38	MTA3	chr1:223316725-223317539	GM12878	blood:	n/a	n/a
39	TBP	chr1:223316445-223317491	GM12878	blood:	n/a	n/a
40	RUNX3	chr1:223316951-223317582	GM12878	blood:	n/a	n/a
41	TAF1	chr1:223316455-223317077	K562	blood:	n/a	n/a
42	NR2F2	chr1:223315904-223317782	K562	blood:	n/a	n/a
43	UBTF	chr1:223316022-223317125	K562	blood:	n/a	n/a
44	MXI1	chr1:223316208-223317544	GM12878	blood:	n/a	n/a
45	MAX	chr1:223315927-223317031	A549	lung:	n/a	chr1:223316630-223316640
46	RCOR1	chr1:223316102-223317525	K562	blood:	n/a	n/a
47	EBF1	chr1:223316235-223317965	GM12878	blood:	n/a	n/a
48	MEF2C	chr1:223316991-223317609	GM12878	blood:	n/a	chr1:223317292-223317306 chr1:223317290-223317305
49	MAX	chr1:223315726-223317814	K562	blood:	n/a	chr1:223316630-223316640
50	MYC	chr1:223316307-223317507	NB4	blood:	n/a	chr1:223316630-223316640

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:

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

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1612431	1.00[AMR][1000 genomes]
rs1613248	1.00[AMR][1000 genomes]
rs1640804	1.00[AMR][1000 genomes]
rs1640806	1.00[AMR][1000 genomes]
rs1640807	1.00[AMR][1000 genomes]
rs1640808	1.00[AMR][1000 genomes]
rs1640862	1.00[AMR][1000 genomes]
rs1773735	1.00[AMR][1000 genomes]
rs1773740	1.00[AMR][1000 genomes]
rs1773741	1.00[AMR][1000 genomes]
rs1773742	1.00[AMR][1000 genomes]
rs1773743	1.00[AMR][1000 genomes]
rs1773745	1.00[AMR][1000 genomes]
rs1773746	1.00[AMR][1000 genomes]
rs1773747	1.00[AMR][1000 genomes]
rs1773748	1.00[AMR][1000 genomes]
rs5744096	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs725083	1.00[AMR][1000 genomes]
rs851159	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:93 , 50 per page) page: 1 2

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	chr1:223315600-223317200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
6	chr1:223315600-223317200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr1:223315600-223317600	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr1:223315800-223317200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr1:223316000-223317200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:223316000-223317200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr1:223316000-223317200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr1:223316000-223317200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:223316000-223317200	Active TSS	Ovary	ovary
14	chr1:223316000-223318200	Enhancers	Fetal Brain Male	brain
15	chr1:223316200-223317400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:223316400-223317200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:223316400-223317600	Flanking Active TSS	GM12878-XiMat	blood
18	chr1:223316400-223318200	Enhancers	Stomach Mucosa	stomach
19	chr1:223316600-223317200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
20	chr1:223316600-223317200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr1:223316600-223317200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:223316600-223317200	Flanking Active TSS	Fetal Brain Female	brain
23	chr1:223316600-223317200	Flanking Active TSS	HSMM	muscle
24	chr1:223316600-223317400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:223316600-223317400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:223316600-223317600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr1:223316600-223317600	Flanking Active TSS	Fetal Heart	heart
28	chr1:223316600-223317800	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr1:223316600-223317800	Enhancers	Gastric	stomach
30	chr1:223316600-223317800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr1:223316600-223318000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr1:223316600-223318000	Enhancers	Spleen	Spleen
33	chr1:223316800-223317200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
34	chr1:223316800-223317200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
35	chr1:223316800-223317200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr1:223316800-223317200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:223316800-223317200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:223316800-223317200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:223316800-223317200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:223316800-223317200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr1:223316800-223317200	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
42	chr1:223316800-223317200	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr1:223316800-223317200	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr1:223316800-223317200	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr1:223316800-223317200	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr1:223316800-223317200	Flanking Active TSS	Right Atrium	heart
47	chr1:223316800-223317200	Flanking Active TSS	Thymus	Thymus
48	chr1:223316800-223317200	Flanking Active TSS	A549	lung
49	chr1:223316800-223317200	Enhancers	Osteobl	bone
50	chr1:223316800-223317400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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