Variant report

Variant	rs1882139
Chromosome Location	chr12:42407659-42407660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1009723	0.81[EUR][1000 genomes]
rs1016659	0.81[EUR][1000 genomes]
rs1024700	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10431604	0.87[EUR][1000 genomes]
rs1069644	0.87[JPT][hapmap]
rs10748323	0.87[EUR][1000 genomes]
rs1226303	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap]
rs1233988	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233992	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1233994	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1233996	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1234032	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1234034	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1234037	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1234038	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1234040	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1234054	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1238290	0.88[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs12826710	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463613	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1628871	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1683195	0.83[MEX][hapmap]
rs1688874	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1732350	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1732351	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1732352	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1994284	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6582378	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712106	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs712119	0.88[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs712120	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs712122	0.86[JPT][hapmap]
rs712123	0.88[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs712125	0.87[JPT][hapmap]
rs712129	0.87[JPT][hapmap]
rs7136038	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303028	0.90[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs7305763	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957081	0.81[EUR][1000 genomes]
rs7958455	0.88[EUR][1000 genomes]
rs7958582	0.90[EUR][1000 genomes]
rs7970115	0.94[JPT][hapmap]
rs824699	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs824716	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs824717	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs824718	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs824724	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs824734	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs824738	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs824741	0.87[JPT][hapmap]
rs844046	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs865420	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap]
rs917666	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv832387	chr12:42345541-42465505	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42402800-42417000	Weak transcription	Right Atrium	heart
2	chr12:42405200-42408800	Weak transcription	Brain Germinal Matrix	brain
3	chr12:42406600-42408800	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:42407200-42409000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:42407200-42409200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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