Variant report

Variant	rs5744102
Chromosome Location	chr1:223316530-223316531
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	chr1:223316479-223316764	Gliobla	brain:	n/a	n/a
2	E2F6	chr1:223315856-223316724	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:223316068-223317528	K562	blood:	n/a	n/a
4	ETS1	chr1:223316139-223316909	K562	blood:	n/a	chr1:223316620-223316629 chr1:223316234-223316248
5	POLR2A	chr1:223316110-223317543	K562	blood:	n/a	n/a
6	ARID3A	chr1:223316397-223317000	K562	blood:	n/a	n/a
7	TAL1	chr1:223316528-223317542	K562	blood:	n/a	n/a
8	EP300	chr1:223316181-223316910	K562	blood:	n/a	chr1:223316519-223316535
9	POLR2A	chr1:223316394-223316764	HUVEC	blood vessel:	n/a	n/a
10	EGR1	chr1:223316049-223316833	K562	blood:	n/a	chr1:223316663-223316677 chr1:223316176-223316189 chr1:223316630-223316640 chr1:223316647-223316657 chr1:223316667-223316676 chr1:223316629-223316643 chr1:223316179-223316189 chr1:223316633-223316643
11	CTCF	chr1:223316188-223316643	NHEK	skin:	n/a	chr1:223316368-223316384 chr1:223316457-223316470
12	ZMIZ1	chr1:223316141-223316847	K562	blood:	n/a	n/a
13	MXI1	chr1:223316528-223316790	K562	blood:	n/a	n/a
14	MAZ	chr1:223315756-223317534	K562	blood:	n/a	chr1:223316630-223316640
15	RAD21	chr1:223316127-223316751	H1-hESC	embryonic stem cell:	n/a	chr1:223316516-223316530
16	E2F6	chr1:223315846-223316860	K562	blood:	n/a	n/a
17	CTCF	chr1:223316149-223316806	GM12878	blood:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
18	POLR2A	chr1:223316319-223316877	ECC-1	luminal epithelium:	n/a	n/a
19	E2F4	chr1:223316005-223316889	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr1:223316253-223316563	ProgFib	skin:	n/a	chr1:223316368-223316384 chr1:223316457-223316470
21	ETS1	chr1:223316302-223316697	K562	blood:	n/a	chr1:223316620-223316629
22	RUNX3	chr1:223316514-223316842	GM12878	blood:	n/a	n/a
23	MAZ	chr1:223316084-223317968	GM12878	blood:	n/a	chr1:223316630-223316640
24	POLR2A	chr1:223316237-223316938	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr1:223316036-223317563	K562	blood:	n/a	chr1:223316630-223316640
26	MYC	chr1:223316510-223316574	K562	blood:	n/a	n/a
27	POLR2A	chr1:223316120-223316948	K562	blood:	n/a	n/a
28	RAD21	chr1:223316262-223316643	Hela-S3	cervix:	n/a	chr1:223316516-223316530
29	RAD21	chr1:223316161-223316584	IMR90	lung:	n/a	chr1:223316516-223316530
30	TBL1XR1	chr1:223316256-223317497	K562	blood:	n/a	n/a
31	CHD2	chr1:223316266-223316732	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:223316455-223316893	A549	lung:	n/a	n/a
33	SIN3AK20	chr1:223316151-223316536	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr1:223316045-223317035	SK-N-MC	brain:	n/a	n/a
35	RFX5	chr1:223316271-223317424	GM12878	blood:	n/a	n/a
36	MAX	chr1:223315978-223316931	MCF-7	breast:	n/a	chr1:223316630-223316640
37	ELF1	chr1:223316212-223316855	K562	blood:	n/a	n/a
38	MAX	chr1:223315843-223317614	GM12878	blood:	n/a	chr1:223316630-223316640
39	BACH1	chr1:223316182-223317057	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr1:223316377-223316872	K562	blood:	n/a	n/a
41	REST	chr1:223316073-223316591	K562	blood:	n/a	n/a
42	POLR2A	chr1:223316292-223316924	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr1:223316168-223316955	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr1:223316392-223316883	GM12878	blood:	n/a	n/a
45	ZNF143	chr1:223316191-223317574	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:223315837-223317506	K562	blood:	n/a	n/a
47	HDAC2	chr1:223316232-223316764	K562	blood:	n/a	n/a
48	CTCF	chr1:223316208-223316556	Gliobla	brain:	n/a	chr1:223316368-223316384 chr1:223316457-223316470
49	RCOR1	chr1:223316311-223316848	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr1:223315622-223317565	K562	blood:	n/a	n/a

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

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

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11485986	1.00[EUR][1000 genomes]
rs11488545	1.00[EUR][1000 genomes]
rs11488546	1.00[EUR][1000 genomes]
rs11488550	1.00[EUR][1000 genomes]
rs1416691	1.00[EUR][1000 genomes]
rs2192616	1.00[EUR][1000 genomes]
rs2609375	1.00[EUR][1000 genomes]
rs2609376	1.00[EUR][1000 genomes]
rs3768284	1.00[EUR][1000 genomes]
rs5744153	1.00[EUR][1000 genomes]
rs61743732	1.00[EUR][1000 genomes]
rs6675057	1.00[EUR][1000 genomes]
rs74145600	1.00[EUR][1000 genomes]
rs851160	1.00[EUR][1000 genomes]
rs851215	1.00[EUR][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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223314800-223316800	Active TSS	Brain Hippocampus Middle	brain
2	chr1:223315200-223317400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr1:223315200-223317600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr1:223315200-223318800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:223315400-223316800	Active TSS	Brain Cingulate Gyrus	brain
6	chr1:223315400-223316800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr1:223315400-223318000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:223315600-223316600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr1:223315600-223316800	Active TSS	Brain Substantia Nigra	brain
10	chr1:223315600-223316800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:223315600-223316800	Active TSS	Rectal Smooth Muscle	rectum
12	chr1:223315600-223317000	Flanking Active TSS	Fetal Muscle Leg	muscle
13	chr1:223315600-223317200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr1:223315600-223317200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr1:223315600-223317600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr1:223315800-223316600	Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr1:223315800-223316600	Active TSS	Brain Germinal Matrix	brain
18	chr1:223315800-223316600	Enhancers	Fetal Heart	heart
19	chr1:223315800-223316800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:223315800-223316800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:223315800-223316800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:223315800-223316800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr1:223315800-223316800	Active TSS	Brain Anterior Caudate	brain
24	chr1:223315800-223316800	Active TSS	Colonic Mucosa	Colon
25	chr1:223315800-223316800	Active TSS	Left Ventricle	heart
26	chr1:223315800-223317000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:223315800-223317000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:223315800-223317000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:223315800-223317000	Flanking Active TSS	Dnd41	blood
30	chr1:223315800-223317200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr1:223316000-223316600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:223316000-223316600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:223316000-223316600	Active TSS	Esophagus	oesophagus
34	chr1:223316000-223316600	Active TSS	Fetal Intestine Small	intestine
35	chr1:223316000-223316600	Active TSS	Gastric	stomach
36	chr1:223316000-223316800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr1:223316000-223316800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:223316000-223316800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:223316000-223316800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:223316000-223316800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:223316000-223316800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:223316000-223316800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:223316000-223316800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:223316000-223316800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:223316000-223316800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:223316000-223316800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:223316000-223316800	Active TSS	Fetal Kidney	kidney
48	chr1:223316000-223316800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr1:223316000-223316800	Active TSS	A549	lung
50	chr1:223316000-223316800	Active TSS	NH-A	brain

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