Variant report

Variant	rs2292762
Chromosome Location	chr1:189837364-189837365
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10753864	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10753865	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10753866	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10753868	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10800667	0.85[ASN][1000 genomes]
rs10800668	0.85[ASN][1000 genomes]
rs10800687	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800688	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919820	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10919868	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919869	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919871	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919881	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12038346	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038351	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405539	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12406391	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356346	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356347	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1589049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2203669	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3005707	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3005710	0.89[CHB][hapmap]
rs3005711	0.89[CHB][hapmap]
rs6672299	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67145011	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67606262	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524192	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7526515	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7540504	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7540796	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7540875	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7548359	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9427455	0.85[ASN][1000 genomes]
rs9427457	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9427458	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9427460	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9427461	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9427703	0.85[ASN][1000 genomes]
rs9427704	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999435	chr1:188997868-189849121	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534452	chr1:189129332-189924389	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1005794	chr1:189488465-190063923	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1009290	chr1:189554045-189908459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv497885	chr1:189562225-190086077	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv868954	chr1:189605447-190135265	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv548532	chr1:189758772-190371671	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv872740	chr1:189765121-189883637	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv997993	chr1:189774125-189939680	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv548543	chr1:189785833-189841516	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3438669	chr1:189821344-189838696	ZNF genes & repeats Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2762203	chr1:189835520-189840518	Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv516072	chr1:189835520-189878594	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1006448	chr1:189835520-189880523	Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2292762	PIP5K1B	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189837200-189837600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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