Variant report

Variant	rs17239020
Chromosome Location	chr15:57295266-57295267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11854006	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12437635	1.00[AFR][1000 genomes]
rs12437714	1.00[AFR][1000 genomes]
rs12437735	1.00[AFR][1000 genomes]
rs12437753	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12437777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12438151	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12438572	1.00[AFR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12439149	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12439165	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12439266	0.80[EUR][1000 genomes]
rs12439547	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12439994	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440116	0.80[EUR][1000 genomes]
rs12440245	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12440699	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12440725	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12440790	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12440891	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12441185	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441200	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12441263	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12441769	1.00[AFR][1000 genomes]
rs12441792	1.00[AFR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12442238	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12442326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442630	1.00[AFR][1000 genomes]
rs12442642	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12442662	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12442839	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12443085	1.00[AFR][1000 genomes]
rs12443125	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1462157	1.00[AFR][1000 genomes]
rs1529597	1.00[AFR][1000 genomes]
rs16977170	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16977201	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17238894	1.00[AFR][1000 genomes]
rs17238901	1.00[AFR][1000 genomes]
rs17238950	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17238971	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17238992	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17239047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239187	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17819616	1.00[AFR][1000 genomes]
rs17819646	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17819658	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819664	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819694	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819779	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2126398	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2585110	0.93[AMR][1000 genomes]
rs4320591	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4362334	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4424865	1.00[AFR][1000 genomes]
rs4514619	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs966807	1.00[AFR][1000 genomes]

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	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	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
4	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
5	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:71 , 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	chr15:57274200-57295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:57278600-57295400	Weak transcription	NH-A	brain
8	chr15:57279400-57300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:57279600-57301800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:57279800-57300200	Weak transcription	Psoas Muscle	Psoas
11	chr15:57282000-57295400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:57282000-57295400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:57282000-57295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:57282000-57307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:57282200-57295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:57282200-57295800	Weak transcription	Fetal Kidney	kidney
18	chr15:57282200-57298600	Weak transcription	Ovary	ovary
19	chr15:57282200-57299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr15:57282200-57308400	Weak transcription	Thymus	Thymus
21	chr15:57282200-57311000	Weak transcription	K562	blood
22	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:57282600-57306200	Weak transcription	HepG2	liver
24	chr15:57283800-57296400	Weak transcription	Fetal Stomach	stomach
25	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:57286000-57295400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:57286000-57296400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:57286000-57299400	Weak transcription	Primary T cells from cord blood	blood
29	chr15:57286000-57299800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:57286000-57306200	Weak transcription	Fetal Intestine Large	intestine
31	chr15:57286000-57307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:57286200-57307600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:57286200-57307600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:57286200-57312000	Weak transcription	HSMM	muscle
35	chr15:57286200-57314800	Weak transcription	Dnd41	blood
36	chr15:57286400-57309400	Weak transcription	Fetal Lung	lung
37	chr15:57288600-57300000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:57288800-57295600	Weak transcription	Brain Anterior Caudate	brain
39	chr15:57288800-57307400	Weak transcription	HMEC	breast
40	chr15:57289200-57295400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:57289400-57304600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:57289400-57308000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:57289600-57315200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:57289600-57315600	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:57289800-57295400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:57289800-57315600	Weak transcription	Primary B cells from cord blood	blood
47	chr15:57292600-57298600	Weak transcription	Left Ventricle	heart
48	chr15:57292600-57300200	Weak transcription	Right Atrium	heart
49	chr15:57292800-57296200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr15:57293600-57295400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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