Variant report

Variant	rs829143
Chromosome Location	chr12:51256065-51256066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10160844	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10459238	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10459239	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747595	0.88[ASN][1000 genomes]
rs10747596	0.87[ASN][1000 genomes]
rs10747597	0.94[ASN][1000 genomes]
rs10747599	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783393	0.93[ASN][1000 genomes]
rs10783394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10783395	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10783405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10783406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876099	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10876100	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10876105	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876115	0.91[ASN][1000 genomes]
rs10876119	0.89[ASN][1000 genomes]
rs1096030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1096031	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1103441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169587	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11169589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11169592	0.92[ASN][1000 genomes]
rs11169593	0.81[EUR][1000 genomes]
rs11169602	0.91[ASN][1000 genomes]
rs11169603	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169608	0.91[ASN][1000 genomes]
rs11169609	0.91[ASN][1000 genomes]
rs11169610	0.91[ASN][1000 genomes]
rs11169612	0.91[ASN][1000 genomes]
rs11169614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11495280	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11533636	0.89[ASN][1000 genomes]
rs12578465	0.89[ASN][1000 genomes]
rs12578466	0.89[ASN][1000 genomes]
rs12581103	0.94[ASN][1000 genomes]
rs1362964	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1583697	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1631348	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1642997	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1643004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1659375	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2554852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2554854	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2579077	1.00[CEU][hapmap]
rs3752667	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4483656	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768926	0.92[ASN][1000 genomes]
rs4768937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768938	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768939	0.94[ASN][1000 genomes]
rs7131969	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73100855	0.93[ASN][1000 genomes]
rs7979616	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829120	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs829122	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs829126	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829128	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829129	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs829132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs829139	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs860476	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs829143	METTL7A	cis	parietal	SCAN
rs829143	IGFBP6	cis	parietal	SCAN
rs829143	RHEBL1	cis	cerebellum	SCAN
rs829143	TUBA1B	cis	cerebellum	SCAN
rs829143	KRT79	cis	cerebellum	SCAN
rs829143	LASS5	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51252000-51259600	Weak transcription	Esophagus	oesophagus
2	chr12:51255400-51256200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:51255800-51256200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:51255800-51256200	Enhancers	NHLF	lung
5	chr12:51255800-51256800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:51255800-51257000	Enhancers	A549	lung
7	chr12:51255800-51257000	Enhancers	Hela-S3	cervix
8	chr12:51256000-51256200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:51256000-51256600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:51256000-51256600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:51256000-51256600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:51256000-51256600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:51256000-51256600	Enhancers	NHEK	skin
14	chr12:51256000-51257000	Enhancers	K562	blood

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