Variant report

Variant	rs6878916
Chromosome Location	chr5:147075533-147075534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10074880	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10463280	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1432827	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432828	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1432829	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1432830	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1594659	0.83[EUR][1000 genomes]
rs17107216	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1835943	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35604260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4476710	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55843547	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56920672	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58854348	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580496	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580497	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67302609	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6869450	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895574	0.89[ASN][1000 genomes]
rs7713466	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7720860	0.85[EUR][1000 genomes]
rs7727216	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7731462	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6878916	SPINK6	cis	lymphoblastoid	seeQTL
rs6878916	JAKMIP2	cis	parietal	SCAN
rs6878916	TNIP1	cis	parietal	SCAN
rs6878916	SCGB3A2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147042000-147076800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:147051400-147076600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:147051600-147075600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:147051600-147077000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:147051600-147078400	Weak transcription	Primary T cells from cord blood	blood
6	chr5:147051800-147076800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:147071600-147077000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:147071600-147077000	Weak transcription	Fetal Stomach	stomach
9	chr5:147071800-147076800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:147072800-147075800	Enhancers	Fetal Lung	lung
11	chr5:147073200-147077000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:147073400-147075800	Enhancers	Fetal Brain Male	brain
13	chr5:147073600-147075600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:147073800-147076000	Enhancers	Brain Substantia Nigra	brain
15	chr5:147073800-147076000	Enhancers	Fetal Brain Female	brain
16	chr5:147074000-147076000	Enhancers	Brain Anterior Caudate	brain
17	chr5:147074200-147076000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:147074200-147076000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:147074200-147076600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:147074400-147077000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:147074600-147081000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:147074800-147076200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:147075200-147075600	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:147075200-147077000	Weak transcription	Brain Angular Gyrus	brain
25	chr5:147075200-147077000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:147075200-147077000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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