Variant report

Variant	rs17238992
Chromosome Location	chr15:57274694-57274695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57273239..57275335-chr15:57275612..57277322,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11854006	0.88[EUR][1000 genomes]
rs12437635	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12437714	1.00[AFR][1000 genomes]
rs12437735	1.00[AFR][1000 genomes]
rs12437753	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12437777	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438151	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12438464	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438572	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12439165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439266	0.84[EUR][1000 genomes]
rs12439547	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440116	0.84[EUR][1000 genomes]
rs12440245	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12440699	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12440725	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440891	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12441185	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441769	1.00[AFR][1000 genomes]
rs12441792	1.00[AFR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs12442042	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12442238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442326	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442630	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12442642	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442662	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442839	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12443125	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12443178	1.00[AFR][1000 genomes]
rs1529597	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs16977170	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16977201	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17238894	1.00[AFR][1000 genomes]
rs17238901	1.00[AFR][1000 genomes]
rs17238950	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17238971	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239020	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];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239068	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239187	1.00[AFR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17819616	1.00[AFR][1000 genomes]
rs17819646	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819658	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819664	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819755	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819779	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819809	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17819946	1.00[AFR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2126398	1.00[AFR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2585110	0.90[AMR][1000 genomes]
rs4320591	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4362334	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4424865	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4514619	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8031866	0.81[EUR][1000 genomes]
rs966807	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:57261200-57279000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:57261400-57275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr15:57262200-57280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:57263800-57276000	Weak transcription	Lung	lung
6	chr15:57264800-57275000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:57264800-57275200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:57265400-57277000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:57269800-57275200	Weak transcription	Right Ventricle	heart
10	chr15:57269800-57276400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:57270000-57276800	Weak transcription	HSMMtube	muscle
13	chr15:57270000-57280200	Weak transcription	Fetal Brain Male	brain
14	chr15:57271200-57276200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:57271400-57275000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:57271400-57276400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:57271600-57275200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:57271600-57275800	Enhancers	Brain Substantia Nigra	brain
19	chr15:57271600-57276600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:57271800-57275000	Weak transcription	HepG2	liver
21	chr15:57271800-57276600	Weak transcription	NHLF	lung
22	chr15:57272000-57275000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:57272000-57275400	Enhancers	A549	lung
24	chr15:57272000-57275800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr15:57272000-57276800	Weak transcription	Hela-S3	cervix
26	chr15:57272200-57276000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr15:57272200-57276600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:57272200-57276600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:57272200-57280600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr15:57272200-57282400	Enhancers	Primary T cells from cord blood	blood
31	chr15:57272400-57276600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:57272600-57275200	Weak transcription	NH-A	brain
33	chr15:57272600-57276400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:57272600-57276800	Weak transcription	HMEC	breast
35	chr15:57272600-57278000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr15:57272800-57274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr15:57272800-57275800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr15:57272800-57276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:57272800-57276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:57273000-57274800	Weak transcription	Osteobl	bone
41	chr15:57273000-57275000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:57273000-57275000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:57273000-57275000	Weak transcription	HSMM	muscle
44	chr15:57273000-57275200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:57273000-57275800	Weak transcription	Left Ventricle	heart
46	chr15:57273000-57276600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:57273000-57276600	Weak transcription	NHEK	skin
48	chr15:57273000-57279400	Weak transcription	Pancreas	Pancrea
49	chr15:57273000-57280800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:57273000-57281400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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