Variant report

Variant	rs2163416
Chromosome Location	chr12:41586605-41586606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10748267	0.90[ASN][1000 genomes]
rs10785186	0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10879831	0.83[ASN][1000 genomes]
rs10879858	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10879867	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10879899	0.82[GIH][hapmap]
rs11180448	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12829840	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1431104	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1431110	0.89[ASN][1000 genomes]
rs1431112	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1527086	0.86[CHB][hapmap]
rs1864611	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1864613	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs281830	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4238081	0.87[ASN][1000 genomes]
rs4767999	0.85[ASN][1000 genomes]
rs4768334	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582240	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs7303285	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs7305919	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7342366	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7954881	0.90[ASN][1000 genomes]
rs7960429	0.86[ASW][hapmap];0.86[GIH][hapmap]
rs7963760	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs975602	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2163416	YAF2	cis	parietal	SCAN
rs2163416	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41585200-41587200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:41585200-41588000	Enhancers	Colon Smooth Muscle	Colon
3	chr12:41585400-41586800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:41585400-41599000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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