Variant report

Variant	rs17575164
Chromosome Location	chr5:42471017-42471018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10059251	1.00[ASN][1000 genomes]
rs10440649	1.00[CHB][hapmap]
rs11957404	1.00[CHB][hapmap]
rs13153060	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13156541	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13168764	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13171720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180731	1.00[ASN][1000 genomes]
rs13182117	1.00[CHB][hapmap]
rs13184352	1.00[CHB][hapmap]
rs13187542	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188386	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13354167	1.00[CHB][hapmap]
rs17574527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17574616	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17636762	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28943878	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28943880	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28943882	1.00[CHB][hapmap]
rs33939197	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34126503	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34161441	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34305870	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34714947	1.00[ASN][1000 genomes]
rs35331831	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35418208	1.00[ASN][1000 genomes]
rs35585211	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35920615	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4129472	1.00[CHB][hapmap]
rs4242100	1.00[ASN][1000 genomes]
rs4242101	1.00[ASN][1000 genomes]
rs4292454	1.00[CHB][hapmap]
rs4320267	1.00[ASN][1000 genomes]
rs4457090	1.00[ASN][1000 genomes]
rs4866836	1.00[ASN][1000 genomes]
rs56781446	1.00[ASN][1000 genomes]
rs61043035	1.00[ASN][1000 genomes]
rs6451618	1.00[ASN][1000 genomes]
rs67005744	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67277863	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67314897	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67846180	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67871277	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6863381	1.00[CHB][hapmap]
rs6872878	1.00[ASN][1000 genomes]
rs6885716	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6891036	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72753062	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72753064	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7702524	1.00[CHB][hapmap]
rs7703669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709790	1.00[CHB][hapmap]
rs7715374	1.00[ASN][1000 genomes]
rs7716495	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7718962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732059	1.00[ASN][1000 genomes]
rs9292848	1.00[ASN][1000 genomes]
rs9292851	1.00[ASN][1000 genomes]
rs9292854	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3334173	chr5:42469395-42471393	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17575164	GYS2	trans	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42454800-42471800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:42455000-42474400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:42455000-42477400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:42462000-42471600	Weak transcription	Fetal Intestine Large	intestine
5	chr5:42462000-42472000	Weak transcription	Fetal Lung	lung
6	chr5:42462200-42471600	Weak transcription	Psoas Muscle	Psoas
7	chr5:42462200-42472200	Weak transcription	Fetal Heart	heart
8	chr5:42466800-42472400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:42468200-42472600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:42468400-42484000	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:42469200-42471400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:42469200-42471400	Weak transcription	Fetal Stomach	stomach
13	chr5:42469800-42472400	Weak transcription	Right Ventricle	heart
14	chr5:42470000-42473200	Weak transcription	Adipose Nuclei	Adipose
15	chr5:42470000-42483000	Weak transcription	Liver	Liver
16	chr5:42470800-42471600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr5:42471000-42471400	Enhancers	Ovary	ovary
18	chr5:42471000-42471800	Weak transcription	Aorta	Aorta

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