Variant report

Variant	rs17563872
Chromosome Location	chr5:147121167-147121168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10477342	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11167996	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12653862	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12659905	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13172946	1.00[AFR][1000 genomes]
rs1347149	1.00[JPT][hapmap]
rs1347150	1.00[JPT][hapmap]
rs1549912	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17495305	1.00[AFR][1000 genomes]
rs17496036	1.00[AFR][1000 genomes]
rs17496399	1.00[AFR][1000 genomes]
rs17496550	1.00[AFR][1000 genomes]
rs17497229	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17497858	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497914	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17498180	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17561784	1.00[AFR][1000 genomes]
rs17562343	1.00[AFR][1000 genomes]
rs17563332	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17624756	0.92[EUR][1000 genomes]
rs17703007	0.94[EUR][1000 genomes]
rs2053050	1.00[AFR][1000 genomes]
rs2053052	1.00[AFR][1000 genomes]
rs2116770	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2436427	1.00[JPT][hapmap]
rs28469761	0.94[EUR][1000 genomes]
rs32204	1.00[JPT][hapmap]
rs35130412	1.00[AFR][1000 genomes]
rs35285805	1.00[AFR][1000 genomes]
rs4593256	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705042	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705189	1.00[AFR][1000 genomes]
rs4705190	1.00[AFR][1000 genomes]
rs6873548	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6895952	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71580441	1.00[AFR][1000 genomes]
rs72835149	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7735973	0.94[EUR][1000 genomes]
rs9686888	0.94[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	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17563872	JAKMIP2	cis	Artery Tibial	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147078600-147146000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:147103600-147121800	Weak transcription	Fetal Brain Male	brain
3	chr5:147111800-147126600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:147112000-147126600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:147112600-147122800	Weak transcription	Brain Angular Gyrus	brain
6	chr5:147113000-147121800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:147113000-147121800	Weak transcription	Brain Germinal Matrix	brain
8	chr5:147113000-147131000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:147114800-147122200	Weak transcription	Brain Anterior Caudate	brain
10	chr5:147115000-147123200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:147115600-147126800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:147115600-147127200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:147117400-147155800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:147119400-147122200	Weak transcription	Brain Substantia Nigra	brain
15	chr5:147120200-147122000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:147120200-147122600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:147120200-147122800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:147120200-147123000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:147120400-147124600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:147120600-147122200	Weak transcription	Brain Hippocampus Middle	brain

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