Variant report

Variant	rs12411115
Chromosome Location	chr1:119960376-119960377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10754396	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10923824	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12022215	0.81[ASN][1000 genomes]
rs12024495	0.82[ASN][1000 genomes]
rs12035458	0.87[CHB][hapmap]
rs12217015	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12402935	0.87[CHB][hapmap]
rs12405488	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12411080	0.94[CHB][hapmap]
rs1361530	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1417609	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1417610	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1538988	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1538990	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17023577	0.84[CEU][hapmap]
rs17023641	0.87[CHB][hapmap]
rs1891030	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2050892	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2050893	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2185556	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2211257	0.87[ASN][1000 genomes]
rs2854961	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35311226	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3753258	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3765948	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765952	0.87[CHB][hapmap];0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs3765956	0.87[CHB][hapmap]
rs3795660	0.87[CHB][hapmap]
rs4659003	0.93[CHB][hapmap]
rs4659174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56326451	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57770425	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59522974	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72991465	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv2599	chr1:119935023-119967748	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv946176	chr1:119960027-119989077	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12411115	NHLH2	cis	cerebellum	SCAN
rs12411115	CD58	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119956000-119962200	Weak transcription	Fetal Intestine Large	intestine
2	chr1:119959800-119961400	Weak transcription	Liver	Liver

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