Variant report

Variant	rs72749554
Chromosome Location	chr1:224003933-224003934
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr1:224003450-224003977	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:224003503-224004036	SK-N-SH	brain:	n/a	n/a
3	FOS	chr1:224003530-224003957	MCF10A-Er-Src	breast:	n/a	n/a
4	PBX3	chr1:224003446-224004021	SK-N-SH	brain:	n/a	n/a
5	JUND	chr1:224003457-224004037	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr1:224003562-224003956	H1-neurons	neurons:	n/a	n/a
7	JUND	chr1:224003562-224004003	HCT-116	colon:	n/a	n/a
8	NR3C1	chr1:224003525-224004010	A549	lung:	n/a	n/a
9	FOSL2	chr1:224003571-224004003	SK-N-SH	brain:	n/a	n/a
10	MAX	chr1:224003469-224004017	HCT-116	colon:	n/a	n/a
11	FOS	chr1:224003556-224003956	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr1:224003581-224003955	MCF10A-Er-Src	breast:	n/a	n/a
13	FOSL2	chr1:224003629-224003935	A549	lung:	n/a	n/a
14	MYC	chr1:224003835-224004013	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224002406..224004329-chr1:224268091..224270003,2	K562	blood:
2	chr1:224000840..224004910-chr1:224006824..224010402,6	K562	blood:
3	chr1:224001116..224004491-chr1:224031166..224035522,4	K562	blood:

No data

Variant related genes	Relation type
TP53BP2	TF binding region
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1153927	0.91[EUR][1000 genomes]
rs1153929	0.92[EUR][1000 genomes]
rs1153930	0.92[EUR][1000 genomes]
rs1153933	0.90[EUR][1000 genomes]
rs1153934	0.89[EUR][1000 genomes]
rs1153936	0.89[EUR][1000 genomes]
rs1153937	0.84[EUR][1000 genomes]
rs1153938	0.84[EUR][1000 genomes]
rs1153943	0.85[EUR][1000 genomes]
rs1153947	0.87[EUR][1000 genomes]
rs1153949	0.88[EUR][1000 genomes]
rs1153971	0.92[EUR][1000 genomes]
rs1153973	0.94[EUR][1000 genomes]
rs12130788	1.00[AFR][1000 genomes]
rs12130866	1.00[AFR][1000 genomes]
rs12132879	1.00[AFR][1000 genomes]
rs1222120	0.89[EUR][1000 genomes]
rs1222121	0.89[EUR][1000 genomes]
rs1222124	0.92[EUR][1000 genomes]
rs1222128	0.92[EUR][1000 genomes]
rs1222146	0.87[EUR][1000 genomes]
rs1222156	0.83[EUR][1000 genomes]
rs1621129	0.85[EUR][1000 genomes]
rs1629850	0.82[EUR][1000 genomes]
rs16842270	0.92[EUR][1000 genomes]
rs16842294	0.90[EUR][1000 genomes]
rs1981171	0.88[EUR][1000 genomes]
rs1982610	0.90[EUR][1000 genomes]
rs1982612	0.90[EUR][1000 genomes]
rs1982613	0.90[EUR][1000 genomes]
rs2242188	0.90[EUR][1000 genomes]
rs28370004	1.00[AFR][1000 genomes]
rs28370163	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370164	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370167	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370172	0.87[EUR][1000 genomes]
rs3738370	0.86[EUR][1000 genomes]
rs3767709	0.94[EUR][1000 genomes]
rs4653457	0.87[EUR][1000 genomes]
rs4653566	1.00[AFR][1000 genomes]
rs56329085	0.90[EUR][1000 genomes]
rs56918361	0.92[EUR][1000 genomes]
rs59104475	0.90[EUR][1000 genomes]
rs59196624	0.89[EUR][1000 genomes]
rs60131749	0.88[EUR][1000 genomes]
rs60164080	0.89[EUR][1000 genomes]
rs6675712	0.87[EUR][1000 genomes]
rs6687003	0.87[EUR][1000 genomes]
rs6694214	0.87[EUR][1000 genomes]
rs72747938	1.00[AFR][1000 genomes]
rs72747945	1.00[AFR][1000 genomes]
rs72749511	1.00[AFR][1000 genomes]
rs72749512	1.00[AFR][1000 genomes]
rs72749513	1.00[AFR][1000 genomes]
rs72749569	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72749591	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs750873	0.83[EUR][1000 genomes]
rs7536779	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:223985400-224004000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:223988200-224012000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:223990600-224007000	Weak transcription	Fetal Brain Male	brain
9	chr1:223991000-224004400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:223991200-224007400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:223991200-224007400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:223991200-224010800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:223991400-224007600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:223993400-224008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:223994600-224007000	Weak transcription	Colonic Mucosa	Colon
16	chr1:223994600-224008200	Weak transcription	Psoas Muscle	Psoas
17	chr1:223995800-224009400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:223996000-224007600	Weak transcription	Hela-S3	cervix
19	chr1:223997200-224004600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:223999200-224004000	Strong transcription	Fetal Lung	lung
21	chr1:223999400-224004000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:223999600-224007800	Weak transcription	Brain Angular Gyrus	brain
23	chr1:223999800-224004800	Strong transcription	Fetal Intestine Large	intestine
24	chr1:223999800-224010800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:224000200-224007400	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:224000800-224004000	Strong transcription	Primary B cells from cord blood	blood
27	chr1:224000800-224004000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:224001000-224010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:224001400-224004000	Genic enhancers	Primary T cells from cord blood	blood
30	chr1:224001400-224007600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:224001400-224008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:224001600-224006800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:224001800-224010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:224001800-224010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:224002000-224004000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:224002000-224004200	Enhancers	HSMMtube	muscle
37	chr1:224002000-224005600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:224002000-224005800	Weak transcription	Fetal Stomach	stomach
39	chr1:224002000-224006800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:224002000-224006800	Weak transcription	Adipose Nuclei	Adipose
41	chr1:224002000-224006800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:224002000-224007600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:224002000-224007600	Weak transcription	Fetal Kidney	kidney
44	chr1:224002000-224007600	Weak transcription	Lung	lung
45	chr1:224002000-224007600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:224002000-224008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:224002000-224008200	Weak transcription	Spleen	Spleen
48	chr1:224002000-224008400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:224002000-224015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:224002000-224023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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