Variant report

Variant	rs11241942
Chromosome Location	chr5:127122492-127122493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10519953	0.95[CEU][hapmap];0.87[TSI][hapmap]
rs10519960	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10900792	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11241939	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957799	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1228156	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12652197	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12653785	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1399829	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421747	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515640	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1560673	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs173581	0.81[ASN][1000 genomes]
rs1849938	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1897525	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248689	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[TSI][hapmap]
rs248692	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.92[TSI][hapmap]
rs248709	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs248716	0.81[EUR][1000 genomes]
rs248722	0.80[EUR][1000 genomes]
rs248724	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs248731	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248733	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248740	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248742	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2569146	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2569148	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2673772	0.90[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57883466	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59513079	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62373501	0.81[EUR][1000 genomes]
rs62373502	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6595789	0.81[EUR][1000 genomes]
rs7714847	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs790827	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs812059	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv965610	chr5:127122488-127132347	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11241942	SLC12A2	cis	cerebellum	SCAN
rs11241942	LYRM7	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127120000-127123000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:127120600-127122600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:127120800-127122800	Bivalent Enhancer	NH-A	brain
4	chr5:127121400-127122800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:127121400-127125400	Weak transcription	Stomach Mucosa	stomach
6	chr5:127122000-127124200	Weak transcription	NHDF-Ad	bronchial
7	chr5:127122400-127123000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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