Variant report

Variant	rs12440878
Chromosome Location	chr15:57535215-57535216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10518910	1.00[CEU][hapmap]
rs1122890	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12438324	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438331	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438428	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438782	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438954	1.00[AFR][1000 genomes]
rs12439017	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12439374	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12440036	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440699	1.00[CEU][hapmap]
rs12440729	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441107	1.00[AFR][1000 genomes]
rs12441239	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442042	0.83[AMR][1000 genomes]
rs12442326	1.00[CEU][hapmap]
rs12442521	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442879	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12443076	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12443085	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12443097	1.00[AFR][1000 genomes]
rs1462157	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239187	1.00[CEU][hapmap]
rs17239313	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239522	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17239543	1.00[AFR][1000 genomes]
rs17819809	1.00[CEU][hapmap]
rs17819994	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820006	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17820077	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820119	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17820131	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2126398	1.00[CEU][hapmap]
rs2414499	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4320591	1.00[CEU][hapmap]
rs4514619	1.00[CEU][hapmap]
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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:57519600-57544600	Weak transcription	Psoas Muscle	Psoas
4	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:57520800-57544600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57521000-57538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:57521400-57536800	Weak transcription	Small Intestine	intestine
8	chr15:57522200-57536200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
10	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
11	chr15:57524400-57535600	Strong transcription	HSMM	muscle
12	chr15:57524400-57540600	Strong transcription	Primary T cells from cord blood	blood
13	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
14	chr15:57526000-57537400	Weak transcription	Esophagus	oesophagus
15	chr15:57526000-57539000	Weak transcription	Gastric	stomach
16	chr15:57526000-57539200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:57526000-57539200	Weak transcription	Lung	lung
18	chr15:57526000-57542600	Weak transcription	Right Ventricle	heart
19	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:57526400-57536000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:57526400-57537200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:57526400-57539200	Weak transcription	Aorta	Aorta
23	chr15:57526600-57537200	Weak transcription	Colonic Mucosa	Colon
24	chr15:57526600-57539000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:57526600-57545400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
28	chr15:57526800-57537200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:57526800-57545400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:57527200-57537400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:57527200-57538200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:57527400-57537600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:57527600-57536000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:57528200-57535600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr15:57528200-57535600	Weak transcription	Osteobl	bone
37	chr15:57528200-57537200	Weak transcription	HepG2	liver
38	chr15:57528200-57537200	Weak transcription	K562	blood
39	chr15:57528200-57537400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:57528200-57537400	Weak transcription	HSMMtube	muscle
41	chr15:57528200-57545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:57528400-57535600	Weak transcription	Fetal Intestine Large	intestine
43	chr15:57528400-57536000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:57528400-57536800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:57528400-57537400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:57528400-57538600	Weak transcription	Ovary	ovary
47	chr15:57528400-57545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:57528400-57554800	Weak transcription	NHEK	skin
49	chr15:57528600-57535600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:57528600-57535600	Weak transcription	Primary T cells fromperipheralblood	blood

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