Variant report

Variant	rs2660801
Chromosome Location	chr3:100912861-100912862
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12485950	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168361	0.86[ASN][1000 genomes]
rs17402964	0.87[JPT][hapmap]
rs187001	0.96[ASN][1000 genomes]
rs187002	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187351	0.86[ASN][1000 genomes]
rs1994202	0.86[ASN][1000 genomes]
rs2460722	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2460723	1.00[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2627548	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627550	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2660800	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2660802	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2660804	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2930448	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348859	0.98[EUR][1000 genomes]
rs348862	0.86[ASN][1000 genomes]
rs348863	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348867	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.97[EUR][1000 genomes]
rs348868	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs348877	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.97[EUR][1000 genomes]
rs348878	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.97[EUR][1000 genomes]
rs348882	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.97[EUR][1000 genomes]
rs348883	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.97[EUR][1000 genomes]
rs4270483	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440103	0.86[ASN][1000 genomes]
rs4683872	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486814	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs488679	1.00[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs494593	0.95[EUR][1000 genomes]
rs511575	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs512553	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518813	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs521661	0.97[EUR][1000 genomes]
rs537271	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538280	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs543560	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs556820	0.83[LWK][hapmap]
rs6441594	0.97[EUR][1000 genomes]
rs7613046	1.00[CEU][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs7634351	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906381	0.86[ASN][1000 genomes]
rs906382	0.86[ASN][1000 genomes]
rs9825713	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877262	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2754039	chr3:100882310-100981310	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2660801	FAM172B	cis	parietal	SCAN
rs2660801	RG9MTD1	cis	parietal	SCAN
rs2660801	IMPG2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100904600-100914600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:100910800-100913400	Enhancers	Osteobl	bone
3	chr3:100911800-100913400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:100911800-100913400	Enhancers	NHEK	skin
5	chr3:100912000-100913800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:100912400-100913000	Enhancers	HSMM	muscle
7	chr3:100912400-100913400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:100912400-100913400	Enhancers	NHDF-Ad	bronchial
9	chr3:100912400-100913600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:100912600-100913000	Enhancers	A549	lung
11	chr3:100912600-100913200	Enhancers	NH-A	brain
12	chr3:100912600-100913200	Enhancers	NHLF	lung
13	chr3:100912600-100913400	Enhancers	HMEC	breast
14	chr3:100912600-100913800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:100912600-100916400	Enhancers	HSMMtube	muscle
16	chr3:100912800-100913000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:100912800-100913000	Enhancers	Hela-S3	cervix
18	chr3:100912800-100913000	Enhancers	HUVEC	blood vessel
19	chr3:100912800-100913400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:100912800-100913400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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