Variant report

Variant	rs2299199
Chromosome Location	chr7:87741514-87741515
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10227241	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229877	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10234048	0.85[CEU][hapmap];0.86[CHB][hapmap];0.89[MEX][hapmap]
rs10234412	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs10272494	0.83[ASN][1000 genomes]
rs10281274	1.00[ASN][1000 genomes]
rs10952910	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs10952911	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10952913	0.96[CEU][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes]
rs10952914	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs11768853	0.83[EUR][1000 genomes]
rs11770825	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535312	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12535365	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12537586	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12540117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13245213	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2008834	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2008840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2097918	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2237541	0.96[CEU][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs2282955	0.89[CEU][hapmap]
rs2282956	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2282957	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs2299198	0.84[EUR][1000 genomes]
rs2299200	0.96[CEU][hapmap];0.85[GIH][hapmap];0.82[EUR][1000 genomes]
rs2301998	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753103	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs3753106	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4442059	0.88[CEU][hapmap]
rs4727151	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs4727152	0.89[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4728731	0.89[CEU][hapmap]
rs6465129	0.96[ASN][1000 genomes]
rs6951172	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[MEX][hapmap]
rs6955194	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs6955696	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs6957754	0.84[EUR][1000 genomes]
rs6958024	0.89[CEU][hapmap]
rs6968026	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[MEX][hapmap]
rs726328	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777040	0.89[CEU][hapmap]
rs7792853	0.84[EUR][1000 genomes]
rs7793051	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793308	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7799148	0.89[CEU][hapmap]
rs9632709	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[MEX][hapmap]
rs9641023	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9691240	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs989616	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023352	chr7:87418818-88192925	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539005	chr7:87418818-88192925	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv525073	chr7:87535096-87812968	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299199	ADAM22	cis	Muscle Skeletal	GTEx
rs2299199	RFX6	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87739000-87745600	Weak transcription	Psoas Muscle	Psoas
2	chr7:87739200-87741800	Weak transcription	Fetal Muscle Leg	muscle
3	chr7:87740600-87741600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr7:87741200-87743000	Enhancers	Fetal Stomach	stomach
5	chr7:87741200-87782600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:87741400-87741600	Flanking Active TSS	Fetal Lung	lung
7	chr7:87741400-87741600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr7:87741400-87741800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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