Variant report

Variant	rs12438428
Chromosome Location	chr15:57492028-57492029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57489288..57492189-chr15:57492368..57494008,2	MCF-7	breast:
2	chr15:57489296..57493196-chr15:57493593..57496438,4	K562	blood:
3	chr15:57491334..57495003-chr15:57497716..57500211,4	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10518910	1.00[CEU][hapmap]
rs1122890	1.00[CEU][hapmap]
rs12437777	1.00[AFR][1000 genomes]
rs12438151	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12438324	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12438331	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438464	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12438782	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes]
rs12439017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439374	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12440036	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440116	0.84[EUR][1000 genomes]
rs12440699	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12440729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440878	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441185	1.00[CEU][hapmap]
rs12441239	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442326	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12442521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442879	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12443076	1.00[CEU][hapmap]
rs12443085	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1462157	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977201	1.00[CEU][hapmap]
rs17239047	1.00[AFR][1000 genomes]
rs17239068	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes]
rs17239187	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17239313	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17239522	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs17819755	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17819779	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17819809	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs17819994	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820006	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820077	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820119	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820131	0.87[AMR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes]
rs2126398	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2414499	1.00[CEU][hapmap]
rs4320591	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[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]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57444400-57507400	Weak transcription	K562	blood
2	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:57457200-57499400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
5	chr15:57459200-57492600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:57477000-57492800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:57478200-57493200	Weak transcription	HepG2	liver
8	chr15:57478600-57494000	Weak transcription	Pancreas	Pancrea
9	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
10	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
12	chr15:57483000-57493800	Weak transcription	Colonic Mucosa	Colon
13	chr15:57484600-57493200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:57484800-57496200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:57484800-57502000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:57485000-57501000	Weak transcription	Spleen	Spleen
17	chr15:57485000-57501800	Weak transcription	Lung	lung
18	chr15:57485000-57506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:57485600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:57485800-57493600	Weak transcription	A549	lung
21	chr15:57486600-57493400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:57486600-57496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:57486800-57493000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:57486800-57505800	Weak transcription	NHDF-Ad	bronchial
25	chr15:57487000-57496600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
27	chr15:57487200-57503000	Weak transcription	Liver	Liver
28	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:57488400-57494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:57488400-57496000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:57488400-57496000	Weak transcription	Fetal Intestine Small	intestine
33	chr15:57489200-57496000	Weak transcription	Osteobl	bone
34	chr15:57489200-57506000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:57489400-57506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:57489600-57492400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:57489800-57493400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr15:57489800-57494200	Strong transcription	Dnd41	blood
39	chr15:57490000-57492200	Enhancers	Small Intestine	intestine
40	chr15:57490200-57494400	Enhancers	Brain Hippocampus Middle	brain
41	chr15:57490600-57492200	Enhancers	Fetal Lung	lung
42	chr15:57490600-57505800	Weak transcription	NH-A	brain
43	chr15:57490800-57492400	Enhancers	Fetal Muscle Leg	muscle
44	chr15:57490800-57496400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:57491000-57492400	Enhancers	Left Ventricle	heart
46	chr15:57491000-57493800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:57491000-57495000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr15:57491000-57501400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:57491000-57505600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:57491000-57506000	Weak transcription	HMEC	breast

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