Variant report

Variant	rs13415601
Chromosome Location	chr2:211080124-211080125
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10179268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192315	1.00[ASN][1000 genomes]
rs1155845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11678206	1.00[ASN][1000 genomes]
rs11682370	1.00[ASN][1000 genomes]
rs11686587	1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs11688180	1.00[ASN][1000 genomes]
rs11688922	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs11900095	0.82[EUR][1000 genomes]
rs12989455	1.00[ASN][1000 genomes]
rs12992714	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002602	1.00[ASN][1000 genomes]
rs13006132	1.00[ASN][1000 genomes]
rs13009071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[ASN][1000 genomes]
rs13009890	1.00[ASN][1000 genomes]
rs13011543	1.00[ASN][1000 genomes]
rs13015354	1.00[ASN][1000 genomes]
rs13015487	0.82[EUR][1000 genomes]
rs13017647	1.00[ASN][1000 genomes]
rs13017752	1.00[ASN][1000 genomes]
rs13018349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs13019613	1.00[ASN][1000 genomes]
rs13020232	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13022638	0.82[EUR][1000 genomes]
rs13023313	0.82[EUR][1000 genomes]
rs13025700	1.00[CHB][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1509570	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844058	1.00[ASN][1000 genomes]
rs16844213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2048277	0.82[EUR][1000 genomes]
rs2160020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs2539005	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263668	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs263680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263686	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34334556	1.00[ASN][1000 genomes]
rs34678259	1.00[ASN][1000 genomes]
rs34693593	0.82[EUR][1000 genomes]
rs35125543	1.00[ASN][1000 genomes]
rs36080651	1.00[ASN][1000 genomes]
rs62202972	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435561	1.00[ASN][1000 genomes]
rs6714161	1.00[ASN][1000 genomes]
rs6716836	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6732486	1.00[ASN][1000 genomes]
rs6732506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6735292	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749996	1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs6754591	1.00[ASN][1000 genomes]
rs6760874	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71350736	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71350737	0.82[EUR][1000 genomes]
rs7557043	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7609345	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	esv1795338	chr2:210758078-211098113	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv1802749	chr2:210905194-211255611	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv1803710	chr2:211073376-211173763	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13415601	PLEKHM3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211051000-211086600	Weak transcription	Adipose Nuclei	Adipose
2	chr2:211052200-211085600	Weak transcription	Aorta	Aorta
3	chr2:211060200-211086600	Weak transcription	Pancreas	Pancrea
4	chr2:211060400-211089000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:211067800-211089200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:211075000-211080200	Weak transcription	Liver	Liver
7	chr2:211079400-211080400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr2:211079400-211080600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:211079600-211080400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr2:211079600-211080400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:211079800-211080200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:211079800-211080200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:211079800-211080400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:211079800-211080600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:211080000-211080200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:211080000-211080200	Enhancers	Gastric	stomach
17	chr2:211080000-211080400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:211080000-211080400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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