Variant report

Variant	rs12440790
Chromosome Location	chr15:57288515-57288516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57286745..57288660-chr15:57302090..57304157,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11854006	0.88[EUR][1000 genomes]
rs12437635	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12437714	1.00[AFR][1000 genomes]
rs12437735	1.00[AFR][1000 genomes]
rs12437753	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12437777	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438151	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12438464	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438572	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439149	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12439165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439266	0.84[EUR][1000 genomes]
rs12439547	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440116	0.84[EUR][1000 genomes]
rs12440245	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12440699	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12440725	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440891	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12441185	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441200	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441263	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441769	1.00[AFR][1000 genomes]
rs12441792	1.00[AFR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12442238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442326	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442630	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12442642	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442662	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442839	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12443125	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12443178	1.00[AFR][1000 genomes]
rs1462157	1.00[CEU][hapmap]
rs1529597	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs16977170	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16977201	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17238894	1.00[AFR][1000 genomes]
rs17238901	1.00[AFR][1000 genomes]
rs17238950	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17238971	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17238992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17239020	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17239047	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239068	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239187	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17819616	1.00[AFR][1000 genomes]
rs17819646	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819658	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819664	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819755	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819779	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819809	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2126398	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2585110	0.90[AMR][1000 genomes]
rs4320591	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4362334	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4424865	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4514619	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8031866	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs966807	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57273000-57307200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:57274200-57289200	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:57274200-57295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:57276200-57289200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr15:57276800-57288600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:57278600-57295400	Weak transcription	NH-A	brain
11	chr15:57279400-57300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:57279600-57301800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:57279800-57300200	Weak transcription	Psoas Muscle	Psoas
14	chr15:57280600-57294000	Weak transcription	HSMMtube	muscle
15	chr15:57282000-57289200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:57282000-57289800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:57282000-57295400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:57282000-57295400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:57282000-57295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:57282000-57307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:57282200-57291800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:57282200-57295000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:57282200-57295200	Weak transcription	Hela-S3	cervix
25	chr15:57282200-57295200	Weak transcription	NHLF	lung
26	chr15:57282200-57295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:57282200-57295800	Weak transcription	Fetal Kidney	kidney
28	chr15:57282200-57298600	Weak transcription	Ovary	ovary
29	chr15:57282200-57299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr15:57282200-57308400	Weak transcription	Thymus	Thymus
31	chr15:57282200-57311000	Weak transcription	K562	blood
32	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:57282400-57288600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:57282600-57289800	Strong transcription	Fetal Thymus	thymus
35	chr15:57282600-57293800	Weak transcription	Fetal Heart	heart
36	chr15:57282600-57306200	Weak transcription	HepG2	liver
37	chr15:57283400-57291800	Weak transcription	Left Ventricle	heart
38	chr15:57283400-57291800	Weak transcription	Right Atrium	heart
39	chr15:57283800-57296400	Weak transcription	Fetal Stomach	stomach
40	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:57285800-57289000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:57286000-57289200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:57286000-57290400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:57286000-57295200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:57286000-57295400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:57286000-57296400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:57286000-57299400	Weak transcription	Primary T cells from cord blood	blood
48	chr15:57286000-57299800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr15:57286000-57306200	Weak transcription	Fetal Intestine Large	intestine
50	chr15:57286000-57307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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