Variant report

Variant	rs2954029
Chromosome Location	chr8:126490972-126490973
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:126441090..126444547-chr8:126489407..126493139,4	MCF-7	breast:
2	chr8:126440471..126443261-chr8:126490513..126492965,2	K562	blood:
3	chr8:126490852..126493614-chr8:126495231..126496917,2	K562	blood:
4	chr8:126490839..126493464-chr8:126493478..126495853,2	MCF-7	breast:
5	chr8:126440590..126444026-chr8:126489711..126492773,5	K562	blood:

Variant related genes	Relation type
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10808546	0.89[EUR][1000 genomes]
rs17321515	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2001844	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2001846	0.88[ASN][1000 genomes]
rs2001945	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2954017	0.84[ASN][1000 genomes]
rs2954019	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2954021	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2954022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2954031	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980853	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980854	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2980855	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2980856	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2980860	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2980868	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980869	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980871	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2980875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2980882	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980886	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6982502	0.88[ASN][1000 genomes]
rs6982636	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6999569	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891437	chr8:126470817-126629328	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3345362	chr8:126489195-126491743	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	esv3428781	chr8:126489395-126491618	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

Variant related diseases (count:11)

Disease	PMID	Source
LDL cholesterol	20686565	GWAS catalog
Triglycerides	19060906	GWAS catalog
Triglycerides	20139978	GWAS catalog
Triglycerides	20864672	GWAS catalog
Cholesterol, total	24097068	GWAS catalog
Triglycerides	24097068	GWAS catalog
LDL cholesterol	24097068	GWAS catalog
HDL cholesterol	20686565	GWAS catalog
HDL cholesterol	24097068	GWAS catalog
Triglycerides	20686565	GWAS catalog
Cholesterol, total	20686565	GWAS catalog

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126483000-126498200	Weak transcription	Right Atrium	heart
2	chr8:126483400-126496600	Weak transcription	Hela-S3	cervix
3	chr8:126487200-126492400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:126487600-126491800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:126487600-126492000	Weak transcription	NHEK	skin
6	chr8:126487600-126493200	Weak transcription	HMEC	breast
7	chr8:126487600-126496600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:126488000-126497200	Weak transcription	Liver	Liver
9	chr8:126489600-126493400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr8:126489800-126491400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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