Variant report

Variant	rs4956517
Chromosome Location	chr4:142043379-142043380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10008705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10016770	0.84[ASN][1000 genomes]
rs10028355	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10029478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1027815	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10519584	0.83[GIH][hapmap]
rs10519586	0.98[EUR][1000 genomes]
rs12509440	0.94[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs13435125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1395668	0.86[ASN][1000 genomes]
rs1395669	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1507178	0.95[EUR][1000 genomes]
rs187139	0.98[EUR][1000 genomes]
rs1873370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs189568	0.98[EUR][1000 genomes]
rs2033612	0.98[EUR][1000 genomes]
rs2321862	0.86[ASN][1000 genomes]
rs28417061	0.95[ASN][1000 genomes]
rs28457672	0.95[ASN][1000 genomes]
rs28628800	0.95[ASN][1000 genomes]
rs28667926	0.82[ASN][1000 genomes]
rs354939	0.95[EUR][1000 genomes]
rs354941	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3913899	0.86[GIH][hapmap]
rs4123363	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4267811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs4386678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs4613644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4629541	0.94[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs4956512	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4956513	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4956514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs4956515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4956516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4956518	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs62324904	1.00[EUR][1000 genomes]
rs62324905	1.00[EUR][1000 genomes]
rs6537030	0.94[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs6813119	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6817313	0.86[ASN][1000 genomes]
rs6826231	0.86[ASN][1000 genomes]
rs6831578	0.86[ASN][1000 genomes]
rs6835953	0.99[EUR][1000 genomes]
rs6853785	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72724492	1.00[EUR][1000 genomes]
rs756170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7658695	0.86[ASN][1000 genomes]
rs7669929	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7683490	0.86[GIH][hapmap]
rs9790672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9790673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880167	chr4:141616979-142092124	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4956517	MGST2	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142038600-142052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:142038800-142044400	Enhancers	Fetal Heart	heart
3	chr4:142039000-142049200	Weak transcription	Fetal Brain Female	brain
4	chr4:142039400-142051800	Weak transcription	Aorta	Aorta
5	chr4:142039800-142045000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:142039800-142045200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:142039800-142045200	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:142040800-142043600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr4:142041000-142047600	Weak transcription	Spleen	Spleen
10	chr4:142041000-142048600	Weak transcription	Adipose Nuclei	Adipose
11	chr4:142041000-142052200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:142041800-142043600	Enhancers	Right Atrium	heart
13	chr4:142041800-142043800	Enhancers	Left Ventricle	heart
14	chr4:142042000-142043600	Enhancers	Right Ventricle	heart
15	chr4:142042200-142047400	Weak transcription	Psoas Muscle	Psoas
16	chr4:142042200-142048200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:142042600-142045200	Weak transcription	Ovary	ovary
18	chr4:142042600-142048600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:142042800-142043600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:142042800-142046400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:142042800-142047400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:142043000-142043800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr4:142043200-142043400	Enhancers	Fetal Stomach	stomach
24	chr4:142043200-142043400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr4:142043200-142043600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:142043200-142043800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:142043200-142043800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr4:142043200-142043800	Enhancers	Fetal Lung	lung
29	chr4:142043200-142044000	Enhancers	Colon Smooth Muscle	Colon

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