Variant report

Variant	rs17497858
Chromosome Location	chr5:147111031-147111032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10036585	0.97[AFR][1000 genomes]
rs10037199	0.93[AFR][1000 genomes]
rs10042877	0.93[AFR][1000 genomes]
rs10077132	0.97[AFR][1000 genomes]
rs10476888	0.97[AFR][1000 genomes]
rs10477342	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10477346	0.97[AFR][1000 genomes]
rs10477347	0.97[AFR][1000 genomes]
rs11167996	0.85[EUR][1000 genomes]
rs12653862	0.92[EUR][1000 genomes]
rs12659905	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1347149	1.00[JPT][hapmap]
rs1347150	1.00[JPT][hapmap]
rs1549912	0.85[EUR][1000 genomes]
rs17497229	0.84[EUR][1000 genomes]
rs17497914	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17498180	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17563332	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17563872	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17624756	0.91[EUR][1000 genomes]
rs17703007	0.93[EUR][1000 genomes]
rs2116770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2436427	1.00[JPT][hapmap]
rs28469761	0.93[EUR][1000 genomes]
rs28661528	0.93[AFR][1000 genomes]
rs32204	1.00[JPT][hapmap]
rs4593256	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705042	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6873548	1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes]
rs6895952	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72835149	0.84[EUR][1000 genomes]
rs7735973	0.93[EUR][1000 genomes]
rs9686888	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3444248	chr5:147094808-147116217	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
2	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
3	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
4	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17497858	MRPL45	trans	parietal	SCAN
rs17497858	JAKMIP2	cis	Artery Tibial	GTEx
rs17497858	JAKMIP2	cis	Artery Aorta	GTEx
rs17497858	SH3RF2	cis	parietal	SCAN

Chromatin state (count:29 , 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	chr5:147101600-147114400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:147102000-147111600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:147102000-147112000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:147102200-147114400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:147102600-147111600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:147103600-147111600	Weak transcription	Fetal Brain Female	brain
8	chr5:147103600-147121800	Weak transcription	Fetal Brain Male	brain
9	chr5:147105600-147114200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:147105800-147114400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:147106600-147111200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:147107200-147112800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:147108600-147111200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:147109800-147113400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:147110400-147111200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:147110400-147111200	Enhancers	Brain Anterior Caudate	brain
17	chr5:147110400-147111400	Enhancers	Brain Angular Gyrus	brain
18	chr5:147110400-147113000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:147110400-147113000	Enhancers	Brain Substantia Nigra	brain
20	chr5:147110600-147111200	Enhancers	Brain Cingulate Gyrus	brain
21	chr5:147110600-147111200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr5:147110600-147111200	Enhancers	Stomach Mucosa	stomach
23	chr5:147110600-147112000	Enhancers	Fetal Intestine Small	intestine
24	chr5:147110600-147112200	Enhancers	Duodenum Mucosa	Duodenum
25	chr5:147110800-147111200	Enhancers	Fetal Intestine Large	intestine
26	chr5:147110800-147111400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr5:147110800-147112200	Enhancers	Fetal Lung	lung
28	chr5:147111000-147111400	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr5:147111000-147111600	Flanking Active TSS	Brain Hippocampus Middle	brain

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