Variant report

Variant	rs56112107
Chromosome Location	chr3:50611532-50611533
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	CTCF	chr3:50611507-50611903	K562	blood:	n/a	chr3:50611775-50611784
2	RAD21	chr3:50611471-50611797	HepG2	liver:	n/a	chr3:50611771-50611785
3	RAD21	chr3:50611428-50611856	HepG2	liver:	n/a	chr3:50611771-50611785
4	POLR2A	chr3:50611453-50611799	K562	blood:	n/a	n/a
5	MAX	chr3:50611502-50611771	K562	blood:	n/a	n/a
6	MYC	chr3:50611530-50611796	K562	blood:	n/a	n/a
7	CTCF	chr3:50611500-50612024	K562	blood:	n/a	chr3:50611775-50611784
8	RAD21	chr3:50611521-50611789	K562	blood:	n/a	chr3:50611771-50611785
9	MAZ	chr3:50611476-50611899	K562	blood:	n/a	chr3:50611848-50611858
10	CTCF	chr3:50611467-50611950	K562	blood:	n/a	chr3:50611775-50611784
11	SMC3	chr3:50611479-50611726	K562	blood:	n/a	chr3:50611691-50611698
12	CTCF	chr3:50611532-50611954	K562	blood:	n/a	chr3:50611775-50611784

No.	Distal block	Cell Line	Cell type
1	chr3:50606526..50611586-chr3:50612274..50616724,6	MCF-7	breast:
2	chr3:50610961..50612138-chr3:50651030..50652539,5	K562	blood:
3	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
4	chr3:50607017..50612379-chr3:51423330..51426962,5	MCF-7	breast:
5	chr3:50608156..50612219-chr3:50612794..50616407,4	K562	blood:
6	chr3:50601756..50613871-chr3:50647072..50654542,28	K562	blood:

Variant related genes	Relation type
C3orf18	TF binding region
HEMK1	TF binding region
ENSG00000145050	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000114735	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1038415	1.00[EUR][1000 genomes]
rs107457	1.00[EUR][1000 genomes]
rs1552255	1.00[EUR][1000 genomes]
rs1552256	1.00[EUR][1000 genomes]
rs17051012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051017	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051404	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1843073	1.00[EUR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2262848	1.00[EUR][1000 genomes]
rs2355337	1.00[EUR][1000 genomes]
rs2459450	1.00[EUR][1000 genomes]
rs2609015	1.00[EUR][1000 genomes]
rs2609027	1.00[EUR][1000 genomes]
rs2609030	1.00[EUR][1000 genomes]
rs2675781	1.00[EUR][1000 genomes]
rs2675785	1.00[EUR][1000 genomes]
rs2675823	1.00[EUR][1000 genomes]
rs2675824	1.00[EUR][1000 genomes]
rs2675826	1.00[EUR][1000 genomes]
rs2675833	1.00[EUR][1000 genomes]
rs407164	1.00[EUR][1000 genomes]
rs421689	1.00[EUR][1000 genomes]
rs4234694	1.00[EUR][1000 genomes]
rs4234695	1.00[EUR][1000 genomes]
rs4267639	1.00[EUR][1000 genomes]
rs4340700	1.00[EUR][1000 genomes]
rs4560294	1.00[AMR][1000 genomes]
rs4688704	1.00[EUR][1000 genomes]
rs55723661	1.00[AMR][1000 genomes]
rs55852678	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56198179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56341000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56413944	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57077411	1.00[AMR][1000 genomes]
rs57155820	1.00[AMR][1000 genomes]
rs57756789	1.00[EUR][1000 genomes]
rs57867785	1.00[AMR][1000 genomes]
rs57987466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58231937	1.00[AMR][1000 genomes]
rs58854038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58911362	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59065723	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59337835	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59340349	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59486246	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60132317	1.00[EUR][1000 genomes]
rs60455882	1.00[EUR][1000 genomes]
rs609678	1.00[EUR][1000 genomes]
rs61032466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61455710	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs621975	1.00[EUR][1000 genomes]
rs628865	1.00[EUR][1000 genomes]
rs6446223	1.00[EUR][1000 genomes]
rs650473	1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789552	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833231	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833232	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833239	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833242	1.00[AMR][1000 genomes]
rs73833247	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833248	1.00[AMR][1000 genomes]
rs73833404	1.00[AMR][1000 genomes]
rs73833406	1.00[AMR][1000 genomes]
rs73833886	1.00[AMR][1000 genomes]
rs73833935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833940	1.00[AMR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835535	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835537	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835538	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936714	1.00[EUR][1000 genomes]
rs9840476	1.00[EUR][1000 genomes]
rs9851304	1.00[EUR][1000 genomes]
rs9857033	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50615600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
3	chr3:50607600-50613000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:50607600-50614400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:50607600-50617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:50607800-50611800	Enhancers	Liver	Liver
8	chr3:50607800-50612000	Weak transcription	Ovary	ovary
9	chr3:50607800-50614200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:50607800-50614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:50607800-50615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:50607800-50615200	Weak transcription	Aorta	Aorta
13	chr3:50607800-50620000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
15	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:50608000-50613000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:50608000-50618400	Weak transcription	NH-A	brain
18	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
20	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:50608200-50612800	Weak transcription	HMEC	breast
22	chr3:50608200-50613800	Weak transcription	Brain Substantia Nigra	brain
23	chr3:50608200-50614000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:50608200-50614200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:50608200-50614400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:50608200-50615200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:50608200-50616200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:50608200-50617400	Weak transcription	Fetal Brain Male	brain
29	chr3:50608200-50624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:50608200-50628400	Weak transcription	A549	lung
31	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
32	chr3:50608400-50613000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:50608400-50614800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:50608400-50615000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:50608400-50625600	Weak transcription	NHDF-Ad	bronchial
36	chr3:50608800-50614800	Genic enhancers	Placenta	Placenta
37	chr3:50609200-50620800	Strong transcription	Brain Germinal Matrix	brain
38	chr3:50609400-50612000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:50609800-50611600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:50609800-50611600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:50609800-50611800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr3:50609800-50611800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:50609800-50612200	Genic enhancers	Fetal Intestine Large	intestine
44	chr3:50609800-50612600	Strong transcription	NHLF	lung
45	chr3:50609800-50620600	Strong transcription	Fetal Brain Female	brain
46	chr3:50610000-50611600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:50610000-50611800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:50610000-50612000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:50610000-50612200	Strong transcription	Gastric	stomach
50	chr3:50610000-50613600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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