Variant report

Variant	rs17039448
Chromosome Location	chr2:50149510-50149511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1013597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10495988	0.89[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11125278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11885824	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11902804	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476729	0.89[EUR][1000 genomes]
rs12617277	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12618646	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12995774	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12998798	0.89[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13000689	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13007882	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13016321	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13016900	0.81[ASN][1000 genomes]
rs13022108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13023203	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13023905	0.85[AMR][1000 genomes]
rs13025974	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13028383	0.84[EUR][1000 genomes]
rs1345562	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17039412	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17039430	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17039452	0.89[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17039454	0.89[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17039456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17039472	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17039484	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17039508	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17039581	0.90[MEX][hapmap]
rs17491776	0.81[JPT][hapmap]
rs2241750	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2350803	0.81[ASN][1000 genomes]
rs34533417	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34918442	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35371642	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35373906	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3922898	0.83[EUR][1000 genomes]
rs3935314	0.84[EUR][1000 genomes]
rs4143112	0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57936567	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60884569	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62132409	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62132414	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62132439	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6753652	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6758043	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6758276	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs920033	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs920034	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs920035	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17039448	KLRAQ1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50141600-50175400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:50141600-50187400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:50142000-50151000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:50142200-50151000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:50143000-50151000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:50145000-50151600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:50148800-50150600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:50148800-50151000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:50149000-50150600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:50149400-50154000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:50149400-50156200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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