Variant report

Variant	rs6580493
Chromosome Location	chr5:147059645-147059646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10463279	0.87[ASN][1000 genomes]
rs17107233	0.92[EUR][1000 genomes]
rs1835942	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55681447	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6874858	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874866	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72835155	0.91[EUR][1000 genomes]
rs72835159	0.88[EUR][1000 genomes]
rs72835162	0.86[EUR][1000 genomes]
rs72835163	0.87[EUR][1000 genomes]
rs7708655	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7716745	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723843	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7726900	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6580493	JAKMIP2	cis	cerebellum	SCAN
rs6580493	TNIP1	cis	parietal	SCAN
rs6580493	JUP	trans	lymphoblastoid	seeQTL
rs6580493	CAMK2A	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147039600-147061800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:147042000-147076800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:147051400-147068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:147051400-147070400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:147051400-147076600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:147051600-147066600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:147051600-147075600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:147051600-147077000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:147051600-147078400	Weak transcription	Primary T cells from cord blood	blood
10	chr5:147051800-147076800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:147052000-147059800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:147053400-147064800	Weak transcription	Brain Germinal Matrix	brain
13	chr5:147054200-147064000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:147054400-147065400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:147054600-147061800	Weak transcription	Brain Anterior Caudate	brain
16	chr5:147054600-147065400	Weak transcription	Brain Angular Gyrus	brain
17	chr5:147056400-147065400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:147059200-147061000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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