Variant report

Variant	rs12442879
Chromosome Location	chr15:57524982-57524983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57510591..57512742-chr15:57523126..57525125,2	K562	blood:
2	chr15:57518271..57520593-chr15:57524473..57526151,2	K562	blood:
3	chr15:57524385..57526174-chr15:57527387..57529513,2	K562	blood:
4	chr15:57523231..57525138-chr15:57581607..57583669,2	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

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];0.80[AMR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes]
rs12438324	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438331	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438428	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438782	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes]
rs12439017	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12439374	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12440036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440699	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12440729	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440878	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12442326	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12442521	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];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1462157	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239187	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes]
rs17239313	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239522	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][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]
rs17819886	1.00[AFR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs17819994	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820006	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820077	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820119	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820131	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes]
rs2126398	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes]
rs2414499	1.00[CEU][hapmap]
rs4320591	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4514619	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs8031866	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
2	chr15:57509200-57526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:57511200-57525400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr15:57511600-57525600	Weak transcription	A549	lung
5	chr15:57511600-57528000	Weak transcription	Fetal Heart	heart
6	chr15:57511800-57525800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:57511800-57528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:57512000-57527200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:57513800-57525400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:57516800-57527800	Weak transcription	NHEK	skin
13	chr15:57519600-57528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:57519600-57544600	Weak transcription	Psoas Muscle	Psoas
15	chr15:57519800-57525200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:57519800-57526000	Weak transcription	GM12878-XiMat	blood
17	chr15:57520000-57526200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:57520400-57527400	Weak transcription	Fetal Brain Female	brain
19	chr15:57520400-57529600	Weak transcription	Brain Angular Gyrus	brain
20	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:57520800-57544600	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:57521000-57538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:57521400-57525200	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:57521400-57536800	Weak transcription	Small Intestine	intestine
25	chr15:57521800-57526600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:57522200-57525400	Weak transcription	Aorta	Aorta
27	chr15:57522200-57536200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
29	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
30	chr15:57523000-57525400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:57523000-57527400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:57523200-57527600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:57523200-57527600	Strong transcription	NHDF-Ad	bronchial
34	chr15:57523200-57529400	Weak transcription	Stomach Mucosa	stomach
35	chr15:57523400-57530000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr15:57523600-57527000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:57523800-57525000	Strong transcription	K562	blood
38	chr15:57523800-57525400	Weak transcription	Colonic Mucosa	Colon
39	chr15:57523800-57527000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr15:57523800-57527200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr15:57523800-57527200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:57523800-57527600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:57523800-57532800	Strong transcription	Dnd41	blood
44	chr15:57524000-57526200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:57524000-57527200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:57524000-57527400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:57524000-57527600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:57524000-57529000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:57524200-57526800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:57524200-57526800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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