Variant report

Variant	rs12089582
Chromosome Location	chr1:225603166-225603167
allele	G/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	CEBPB	chr1:225603084-225603374	Hela-S3	cervix:	n/a	chr1:225603212-225603223
2	POLR2A	chr1:225592461-225603516	K562	blood:	n/a	n/a
3	CEBPB	chr1:225603068-225603376	HepG2	liver:	n/a	chr1:225603212-225603223
4	CEBPB	chr1:225603032-225603406	K562	blood:	n/a	chr1:225603212-225603223
5	CEBPB	chr1:225603024-225603332	K562	blood:	n/a	chr1:225603212-225603223
6	CEBPB	chr1:225603036-225603389	IMR90	lung:	n/a	chr1:225603212-225603223
7	CEBPB	chr1:225603099-225603323	A549	lung:	n/a	chr1:225603212-225603223
8	CTCF	chr1:225603120-225603270	AG04450	lung:	n/a	n/a
9	CTCF	chr1:225603100-225603250	HPAF	blood vessel:	n/a	n/a
10	POLR2A	chr1:225603103-225603377	K562	blood:	n/a	n/a
11	CEBPB	chr1:225603042-225603329	MCF-7	breast:	n/a	chr1:225603212-225603223
12	CEBPB	chr1:225603047-225603379	A549	lung:	n/a	chr1:225603212-225603223
13	POLR2A	chr1:225603038-225603730	K562	blood:	n/a	n/a
14	CEBPB	chr1:225603057-225603358	H1-hESC	embryonic stem cell:	n/a	chr1:225603212-225603223
15	POLR2A	chr1:225603105-225603640	K562	blood:	n/a	n/a
16	CEBPB	chr1:225602987-225603516	A549	lung:	n/a	chr1:225603212-225603223
17	CTCF	chr1:225603140-225603290	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225602519..225604665-chr1:225608862..225611080,2	MCF-7	breast:
2	chr1:225602532..225604048-chr1:225605960..225608580,2	MCF-7	breast:

Variant related genes	Relation type
LBR	TF binding region
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12061268	1.00[CHB][hapmap]
rs12081774	1.00[CHB][hapmap]
rs12083979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12085130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12087159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12088235	1.00[CHB][hapmap]
rs12097737	1.00[CHB][hapmap]
rs1537877	1.00[JPT][hapmap]
rs16844841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17558869	1.00[JPT][hapmap]
rs41267357	1.00[AMR][1000 genomes]
rs41268715	0.90[AMR][1000 genomes]
rs41304014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41304141	1.00[AMR][1000 genomes]
rs61738690	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6679318	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 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	chr1:225582200-225610400	Strong transcription	Fetal Thymus	thymus
2	chr1:225584000-225603800	Weak transcription	Psoas Muscle	Psoas
3	chr1:225584200-225610600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:225584800-225609800	Strong transcription	Dnd41	blood
5	chr1:225584800-225610400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:225585000-225610400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:225585200-225609800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:225585800-225610000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:225585800-225610000	Strong transcription	K562	blood
13	chr1:225585800-225610400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:225586000-225607000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:225587600-225607000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:225587600-225607800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:225587800-225610000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:225588200-225605400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:225588200-225608200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:225588200-225610200	Strong transcription	Osteobl	bone
21	chr1:225588400-225604200	Strong transcription	HUVEC	blood vessel
22	chr1:225588600-225608400	Strong transcription	Hela-S3	cervix
23	chr1:225588600-225609800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:225589000-225607400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:225590200-225610000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:225590600-225607200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:225590600-225607400	Strong transcription	Thymus	Thymus
28	chr1:225590600-225607800	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:225590600-225608400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:225590800-225608200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:225591000-225604000	Strong transcription	Fetal Stomach	stomach
32	chr1:225591800-225608200	Strong transcription	Brain Germinal Matrix	brain
33	chr1:225592800-225607400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr1:225593000-225610800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:225594600-225607200	Strong transcription	NHEK	skin
36	chr1:225595400-225610400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:225595600-225607600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:225595800-225608400	Strong transcription	Fetal Brain Female	brain
39	chr1:225596200-225607600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:225596800-225607000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr1:225596800-225607600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:225596800-225610600	Strong transcription	HSMM	muscle
43	chr1:225597000-225607200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:225597400-225603400	Strong transcription	NHDF-Ad	bronchial
45	chr1:225597400-225607600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:225597400-225608600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:225597400-225608600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:225597600-225604600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:225597600-225607000	Strong transcription	Left Ventricle	heart
50	chr1:225597600-225607200	Strong transcription	Adipose Nuclei	Adipose

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