Variant report

Variant	rs12477924
Chromosome Location	chr2:127795944-127795945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11888878	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11893989	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902275	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12465042	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12474412	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476339	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17014784	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17014818	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17014851	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17040070	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2071268	0.96[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2071270	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3768859	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768860	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3820757	0.87[MEX][hapmap]
rs4662703	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4663089	0.96[CEU][hapmap]
rs4663090	0.85[EUR][1000 genomes]
rs55819047	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55999604	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56408880	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60022219	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66507470	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6745677	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67920725	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72481904	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs727095	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72846676	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7570116	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573824	0.92[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs880436	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv459230	chr2:127771006-127844735	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv583032	chr2:127771006-127844735	Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1003730	chr2:127794288-127860830	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1003461	chr2:127794288-127862257	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12477924	POLR2D	cis	parietal	SCAN
rs12477924	MYO7B	cis	parietal	SCAN
rs12477924	AMMECR1L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127783600-127797000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:127783800-127815600	Weak transcription	Aorta	Aorta
3	chr2:127790400-127797000	Weak transcription	GM12878-XiMat	blood
4	chr2:127793200-127801200	Weak transcription	Fetal Lung	lung
5	chr2:127793200-127805400	Weak transcription	Liver	Liver
6	chr2:127794400-127797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:127795000-127796000	Enhancers	Fetal Muscle Leg	muscle
8	chr2:127795000-127796000	Enhancers	Fetal Stomach	stomach
9	chr2:127795600-127801400	Weak transcription	Fetal Heart	heart
10	chr2:127795800-127796400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:127795800-127807600	Weak transcription	Brain Germinal Matrix	brain

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