Variant report

Variant	rs17239089
Chromosome Location	chr15:57323671-57323672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57315197..57318733-chr15:57320688..57324516,3	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11854006	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12437635	1.00[AFR][1000 genomes]
rs12437713	0.86[EUR][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];0.84[EUR][1000 genomes]
rs12437777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438151	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12438428	1.00[AFR][1000 genomes]
rs12438464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438572	1.00[AFR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12439149	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439165	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12439266	0.92[EUR][1000 genomes]
rs12439547	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12439994	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12440116	0.92[EUR][1000 genomes]
rs12440245	1.00[AFR][1000 genomes]
rs12440699	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440725	1.00[AFR][1000 genomes]
rs12440729	1.00[AFR][1000 genomes]
rs12440790	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440891	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12441185	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441200	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441239	1.00[AFR][1000 genomes]
rs12441263	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441769	1.00[AFR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12442238	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442521	1.00[AFR][1000 genomes]
rs12442630	1.00[AFR][1000 genomes]
rs12442642	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12442662	1.00[AFR][1000 genomes]
rs12442839	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12443085	1.00[AFR][1000 genomes]
rs12443125	1.00[AFR][1000 genomes]
rs1462157	1.00[AFR][1000 genomes]
rs1529597	1.00[AFR][1000 genomes]
rs16977170	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16977201	0.85[AMR][1000 genomes];0.96[EUR][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];0.84[EUR][1000 genomes]
rs17238992	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17239068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.96[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17819646	1.00[AFR][1000 genomes]
rs17819658	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819664	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819694	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs17819755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819779	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs17819994	1.00[AFR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2126398	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2585110	0.93[AMR][1000 genomes]
rs4320591	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4362334	1.00[AFR][1000 genomes]
rs4424865	1.00[AFR][1000 genomes]
rs4514619	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs8031866	0.88[EUR][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:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57308000-57328000	Weak transcription	Gastric	stomach
2	chr15:57309400-57334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:57315600-57328200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:57315600-57328600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:57316400-57324000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:57316400-57328200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
9	chr15:57316600-57327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr15:57317600-57326200	Weak transcription	Esophagus	oesophagus
11	chr15:57318600-57323800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:57318600-57331000	Weak transcription	Fetal Kidney	kidney
13	chr15:57318600-57335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:57320600-57325200	Enhancers	Brain Substantia Nigra	brain
15	chr15:57321400-57324600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:57322000-57324400	Enhancers	Fetal Heart	heart
17	chr15:57322400-57324200	Enhancers	Psoas Muscle	Psoas
18	chr15:57322400-57324400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:57322400-57326600	Enhancers	Brain Angular Gyrus	brain
20	chr15:57322600-57324800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr15:57322600-57325000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:57322800-57326200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr15:57323000-57323800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr15:57323000-57324200	Enhancers	Primary T cells from cord blood	blood
25	chr15:57323000-57324200	Enhancers	Primary hematopoietic stem cells	blood
26	chr15:57323000-57324200	Enhancers	Liver	Liver
27	chr15:57323000-57324200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr15:57323000-57324200	Enhancers	HUVEC	blood vessel
29	chr15:57323000-57324200	Enhancers	NHDF-Ad	bronchial
30	chr15:57323000-57324400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr15:57323000-57324400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:57323000-57324400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:57323000-57324400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr15:57323000-57324400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:57323000-57324400	Genic enhancers	Fetal Thymus	thymus
36	chr15:57323000-57324400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr15:57323000-57324400	Enhancers	A549	lung
38	chr15:57323000-57324400	Enhancers	K562	blood
39	chr15:57323000-57324400	Enhancers	NH-A	brain
40	chr15:57323000-57324400	Enhancers	NHLF	lung
41	chr15:57323000-57324600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr15:57323000-57324600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:57323000-57324800	Enhancers	Colon Smooth Muscle	Colon
44	chr15:57323000-57324800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr15:57323000-57325200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:57323200-57323800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:57323200-57323800	Enhancers	Rectal Smooth Muscle	rectum
48	chr15:57323200-57324200	Enhancers	Fetal Lung	lung
49	chr15:57323200-57324200	Genic enhancers	Thymus	Thymus
50	chr15:57323200-57324200	Enhancers	HSMMtube	muscle

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