Variant report

Variant	rs16838380
Chromosome Location	chr1:239662832-239662833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10495443	0.95[EUR][1000 genomes]
rs12117673	0.93[EUR][1000 genomes]
rs12118163	0.91[EUR][1000 genomes]
rs12118164	0.85[EUR][1000 genomes]
rs12118522	0.88[EUR][1000 genomes]
rs12119752	0.90[EUR][1000 genomes]
rs12120600	0.85[EUR][1000 genomes]
rs12125436	0.93[EUR][1000 genomes]
rs12128278	0.93[EUR][1000 genomes]
rs12136103	0.93[EUR][1000 genomes]
rs12136673	0.91[EUR][1000 genomes]
rs12138748	0.91[EUR][1000 genomes]
rs12141123	0.85[EUR][1000 genomes]
rs12142001	0.90[EUR][1000 genomes]
rs12142243	0.85[EUR][1000 genomes]
rs12144838	0.85[EUR][1000 genomes]
rs12239665	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17585014	0.95[EUR][1000 genomes]
rs60281676	0.95[EUR][1000 genomes]
rs72754702	0.93[EUR][1000 genomes]
rs72756703	0.93[EUR][1000 genomes]
rs7522967	0.82[ASN][1000 genomes]
rs946355	0.95[EUR][1000 genomes]
rs946356	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv549436	chr1:239632055-239678115	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	diseases
7	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv549437	chr1:239659953-239677004	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16838380	GPR137B	cis	parietal	SCAN
rs16838380	B3GALNT2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239647000-239665200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:239657400-239675200	Weak transcription	Ovary	ovary
3	chr1:239660800-239664400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:239662200-239663200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr1:239662400-239663000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr1:239662400-239663000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:239662600-239665600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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