Variant report

Variant	rs7544758
Chromosome Location	chr1:216777687-216777688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10218694	0.88[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10863256	0.82[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs10863258	0.82[ASN][1000 genomes]
rs11117627	0.90[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs11117628	0.85[AMR][1000 genomes]
rs12087642	0.83[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12088947	0.88[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1414530	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs1419242	0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1498276	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs1833038	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1833040	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1857401	0.88[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2377106	0.93[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4567343	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs6673566	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs6673588	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs6701062	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs7519402	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7533692	0.93[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546236	0.92[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs7553212	0.86[JPT][hapmap]
rs7553463	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs951034	0.88[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873178	chr1:216714314-216813244	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7544758	SMYD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216775000-216779200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:216775000-216780200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:216775200-216778200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:216775200-216778400	Weak transcription	Fetal Lung	lung
5	chr1:216775200-216779200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:216775200-216779200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:216775200-216779400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:216775200-216779400	Weak transcription	Fetal Stomach	stomach
9	chr1:216775200-216789400	Weak transcription	Right Atrium	heart
10	chr1:216775200-216835400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:216775400-216778600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:216775600-216778200	Weak transcription	Fetal Heart	heart
13	chr1:216775600-216783600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:216777600-216778000	Enhancers	Left Ventricle	heart
15	chr1:216777600-216778200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:216777600-216778400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:216777600-216778400	Enhancers	Fetal Muscle Leg	muscle
18	chr1:216777600-216779000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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