Variant report

Variant	rs2537752
Chromosome Location	chr12:10467533-10467534
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABARAPL1-3	chr12:10467272-10467608	NONHSAT026875

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10845106	0.81[AFR][1000 genomes]
rs11053739	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11053740	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11611333	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12829155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1600126	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1600130	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2270238	0.92[GIH][hapmap]
rs2302489	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2537781	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2617146	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759270	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[EUR][1000 genomes]
rs3759272	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3759273	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3809214	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3867486	0.83[ASN][1000 genomes]
rs3912117	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs3927994	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61242400	0.83[EUR][1000 genomes]
rs7135494	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7301715	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7313418	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7314888	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7316530	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7964452	0.83[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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv605	chr12:10448638-10494208	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2537752	ATN1	cis	parietal	SCAN
rs2537752	NOP2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10454800-10474400	Weak transcription	Left Ventricle	heart
2	chr12:10462800-10471400	Weak transcription	Right Ventricle	heart
3	chr12:10463200-10470800	Weak transcription	Placenta	Placenta
4	chr12:10463800-10470600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:10466200-10469000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:10467400-10472600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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