Variant report

Variant	rs1222128
Chromosome Location	chr1:224002810-224002811
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	FOXA2	chr1:224002720-224003065	HepG2	liver:	n/a	n/a
2	GATA3	chr1:224002600-224003074	MCF-7	breast:	n/a	n/a
3	FOXA1	chr1:224002719-224003103	T-47D	breast:	n/a	chr1:224002908-224002923
4	FOXA1	chr1:224002733-224003097	HepG2	liver:	n/a	chr1:224002908-224002923
5	GATA3	chr1:224002755-224003092	T-47D	breast:	n/a	n/a
6	FOXA1	chr1:224002572-224003080	HepG2	liver:	n/a	chr1:224002908-224002923
7	STAT3	chr1:224002705-224002905	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA1	chr1:224002666-224003039	HepG2	liver:	n/a	chr1:224002908-224002923

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:

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

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1003061	0.89[ASN][1000 genomes]
rs1153927	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153929	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153934	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1153937	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1153938	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1153943	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1153947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153949	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153973	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222120	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1222121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1222124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222146	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1222156	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1621129	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1629850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16842270	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16842294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16842321	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1981171	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1982610	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982613	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28370163	0.91[EUR][1000 genomes]
rs28370164	0.91[EUR][1000 genomes]
rs28370167	0.91[EUR][1000 genomes]
rs28370172	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653457	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56329085	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56918361	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59104475	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59196624	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60131749	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60164080	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60739082	0.88[ASN][1000 genomes]
rs6604726	0.86[ASN][1000 genomes]
rs6661816	0.90[ASN][1000 genomes]
rs6675712	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6687003	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6694214	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72749554	0.92[EUR][1000 genomes]
rs72749569	0.92[EUR][1000 genomes]
rs72749588	0.92[ASN][1000 genomes]
rs737066	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs750873	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7536779	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs898878	0.90[ASN][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:126 , 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	chr1:223976800-224003000	Weak transcription	Fetal Heart	heart
7	chr1:223984200-224003000	Strong transcription	K562	blood
8	chr1:223985400-224004000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:223988200-224012000	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:223990600-224007000	Weak transcription	Fetal Brain Male	brain
11	chr1:223991000-224004400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:223991200-224007400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:223991200-224007400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:223991200-224010800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:223991400-224007600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:223993400-224008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:223994600-224007000	Weak transcription	Colonic Mucosa	Colon
18	chr1:223994600-224008200	Weak transcription	Psoas Muscle	Psoas
19	chr1:223995800-224009400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:223996000-224007600	Weak transcription	Hela-S3	cervix
21	chr1:223997200-224004600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:223998600-224003200	Weak transcription	HMEC	breast
23	chr1:223999000-224003200	Weak transcription	NHDF-Ad	bronchial
24	chr1:223999200-224004000	Strong transcription	Fetal Lung	lung
25	chr1:223999400-224004000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:223999600-224007800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:223999800-224003200	Weak transcription	Right Atrium	heart
28	chr1:223999800-224003400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:223999800-224004800	Strong transcription	Fetal Intestine Large	intestine
30	chr1:223999800-224010800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:224000200-224003200	Weak transcription	NH-A	brain
32	chr1:224000200-224003200	Weak transcription	NHEK	skin
33	chr1:224000200-224007400	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:224000800-224004000	Strong transcription	Primary B cells from cord blood	blood
35	chr1:224000800-224004000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:224001000-224003200	Weak transcription	Aorta	Aorta
37	chr1:224001000-224010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:224001400-224003600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:224001400-224004000	Genic enhancers	Primary T cells from cord blood	blood
40	chr1:224001400-224007600	Weak transcription	Brain Germinal Matrix	brain
41	chr1:224001400-224008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:224001600-224003200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:224001600-224006800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:224001800-224003000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:224001800-224003000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:224001800-224003200	Weak transcription	Right Ventricle	heart
47	chr1:224001800-224003400	Weak transcription	Brain Substantia Nigra	brain
48	chr1:224001800-224010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:224001800-224010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:224002000-224003200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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