Variant report

Variant	rs12438893
Chromosome Location	chr15:57414604-57414605
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57411738..57417145-chr15:57421254..57425802,5	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11854006	0.88[EUR][1000 genomes]
rs12437753	1.00[AFR][1000 genomes]
rs12437777	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12438151	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12438428	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12438464	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12439017	1.00[AFR][1000 genomes]
rs12439149	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12439165	1.00[AFR][1000 genomes]
rs12439266	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439547	1.00[AFR][1000 genomes]
rs12439994	1.00[AFR][1000 genomes]
rs12440036	1.00[AFR][1000 genomes]
rs12440116	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440699	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440729	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12440790	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12441185	0.84[EUR][1000 genomes]
rs12441200	0.84[EUR][1000 genomes]
rs12441239	1.00[AFR][1000 genomes]
rs12441263	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442238	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12442326	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12442521	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12442839	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12442879	1.00[AFR][1000 genomes]
rs12443085	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1462157	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16977201	0.88[EUR][1000 genomes]
rs17238971	1.00[AFR][1000 genomes]
rs17238992	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17239020	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17239047	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17239068	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17239187	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17239313	0.84[EUR][1000 genomes]
rs17819694	1.00[AFR][1000 genomes]
rs17819755	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17819779	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819809	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs17819994	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17820006	0.84[EUR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2126398	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4320591	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4514619	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031866	0.96[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:57382800-57419600	Weak transcription	K562	blood
3	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
6	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
8	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
9	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
10	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
12	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:57404800-57415600	Weak transcription	Thymus	Thymus
16	chr15:57406800-57416200	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:57406800-57425000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:57406800-57425400	Weak transcription	Pancreas	Pancrea
19	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
22	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
23	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:57409400-57415600	Enhancers	Brain Hippocampus Middle	brain
25	chr15:57410200-57414800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr15:57410200-57415200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr15:57410400-57425400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:57410600-57415400	Enhancers	Brain Cingulate Gyrus	brain
29	chr15:57410600-57415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:57410600-57416400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:57410600-57416400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:57410600-57419800	Weak transcription	HepG2	liver
33	chr15:57410600-57421600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr15:57410600-57424800	Weak transcription	HSMMtube	muscle
35	chr15:57410600-57425000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:57410600-57425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:57410600-57426600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:57410600-57440800	Weak transcription	Ovary	ovary
39	chr15:57410800-57415000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:57410800-57416400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:57410800-57425000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:57410800-57425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:57410800-57425600	Weak transcription	HMEC	breast
44	chr15:57411000-57416200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:57411000-57428200	Weak transcription	NHLF	lung
46	chr15:57411000-57430400	Weak transcription	NH-A	brain
47	chr15:57411200-57422000	Weak transcription	Hela-S3	cervix
48	chr15:57411400-57416400	Weak transcription	Dnd41	blood
49	chr15:57411400-57426200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:57411600-57424200	Weak transcription	Brain Germinal Matrix	brain

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