Variant report

Variant	rs3759270
Chromosome Location	chr12:10459191-10459192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10772256	0.80[YRI][hapmap]
rs10845105	0.80[YRI][hapmap]
rs11053738	0.87[EUR][1000 genomes]
rs11053739	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11053740	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11611333	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12829155	0.82[CEU][hapmap]
rs1600126	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1600130	0.89[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2270238	0.90[GIH][hapmap]
rs2302489	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2537752	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[EUR][1000 genomes]
rs2537781	0.92[CEU][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs2617146	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs3759272	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3759273	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3809214	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3863336	0.80[YRI][hapmap]
rs3867486	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3912117	0.89[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs3927994	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61242400	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7135494	0.81[EUR][1000 genomes]
rs7301715	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7313418	0.82[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7314888	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7316530	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7964452	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970821	0.81[TSI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3759270	KLRA1	cis	cerebellum	SCAN
rs3759270	ATN1	cis	parietal	SCAN
rs3759270	NOP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10453200-10461000	Weak transcription	Placenta	Placenta
2	chr12:10454800-10474400	Weak transcription	Left Ventricle	heart
3	chr12:10458000-10464200	Active TSS	Primary T cells fromperipheralblood	blood
4	chr12:10458200-10460600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:10458400-10460400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:10458800-10461200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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