Variant report

Variant	rs6673566
Chromosome Location	chr1:216789386-216789387
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10218694	0.83[MEX][hapmap]
rs10779267	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10779268	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863259	0.86[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12087642	0.83[MEX][hapmap]
rs12088947	0.83[MEX][hapmap]
rs1414529	0.87[JPT][hapmap]
rs1414530	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498277	0.82[JPT][hapmap]
rs1532500	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537810	0.82[JPT][hapmap]
rs1826977	0.82[JPT][hapmap]
rs1857401	0.83[MEX][hapmap]
rs1857404	0.88[AFR][1000 genomes]
rs1857405	0.90[AFR][1000 genomes]
rs1857412	0.87[JPT][hapmap]
rs1857413	0.87[JPT][hapmap]
rs4124653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4295936	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4567343	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6673588	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673703	0.82[JPT][hapmap]
rs7524845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544758	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7553463	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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
rs6673566	SMYD2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216775200-216789400	Weak transcription	Right Atrium	heart
2	chr1:216775200-216835400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:216781200-216792200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:216784400-216790000	Weak transcription	Psoas Muscle	Psoas
5	chr1:216784600-216790400	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:216786200-216789800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:216786200-216789800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:216786400-216789600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:216787400-216853800	Weak transcription	Pancreas	Pancrea
10	chr1:216787600-216789400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:216787600-216790000	Enhancers	Fetal Heart	heart
12	chr1:216787800-216790200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:216788200-216789800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:216788800-216789600	Enhancers	Right Ventricle	heart
15	chr1:216788800-216789800	Enhancers	Left Ventricle	heart
16	chr1:216789200-216789400	Enhancers	Ovary	ovary

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