Variant report

Variant	rs9686888
Chromosome Location	chr5:147147668-147147669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10477342	0.93[EUR][1000 genomes]
rs12653862	0.85[EUR][1000 genomes]
rs12659905	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17497858	0.93[EUR][1000 genomes]
rs17497914	0.90[EUR][1000 genomes]
rs17498180	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17563332	0.86[EUR][1000 genomes]
rs17563872	0.94[EUR][1000 genomes]
rs17624756	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17703007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116770	0.93[EUR][1000 genomes]
rs28469761	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32204	0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4593256	0.93[EUR][1000 genomes]
rs4705042	0.93[EUR][1000 genomes]
rs6873548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895952	0.89[EUR][1000 genomes]
rs7735973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9686888	JAKMIP2	cis	Artery Tibial	GTEx
rs9686888	SH3RF2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147117400-147155800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:147140800-147153200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:147142000-147155600	Weak transcription	Primary B cells from cord blood	blood
4	chr5:147142800-147154600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:147143800-147147800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:147143800-147153000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:147144200-147151200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:147144200-147152400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:147144800-147147800	Enhancers	Brain Substantia Nigra	brain
10	chr5:147145000-147148400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr5:147146800-147150600	Weak transcription	Brain Anterior Caudate	brain
12	chr5:147146800-147160600	Weak transcription	Primary T cells from cord blood	blood
13	chr5:147147000-147148400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:147147000-147150600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:147147000-147151000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:147147000-147156600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:147147200-147158000	Weak transcription	Brain Germinal Matrix	brain
18	chr5:147147400-147154000	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:147147400-147156800	Weak transcription	Brain Angular Gyrus	brain
20	chr5:147147600-147147800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:147147600-147158200	Weak transcription	Brain Inferior Temporal Lobe	brain

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