Variant report

Variant	rs2999503
Chromosome Location	chr1:216879359-216879360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10863269	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs11117646	0.88[CHB][hapmap]
rs11117649	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs11117669	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs12060770	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs12070175	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs17043393	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs17043436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17043466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17043570	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs2066108	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789722	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2813666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2813670	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2813711	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820882	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61817046	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61817047	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538424	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs7543361	0.88[CHB][hapmap];0.80[CHD][hapmap]
rs7550534	0.88[CHB][hapmap]
rs946468	0.88[CHB][hapmap];0.80[CHD][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2999503	SMYD2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216868200-216894000	Weak transcription	Placenta	Placenta
2	chr1:216874400-216879400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:216878800-216879400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr1:216878800-216879600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:216878800-216879600	Enhancers	Fetal Brain Male	brain
6	chr1:216878800-216879600	Enhancers	NHEK	skin
7	chr1:216878800-216879800	Enhancers	Fetal Brain Female	brain
8	chr1:216878800-216880000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:216879000-216879400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:216879000-216879400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:216879000-216879400	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr1:216879000-216879400	Enhancers	Gastric	stomach
13	chr1:216879000-216879600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:216879000-216879600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:216879000-216879800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:216879000-216879800	Enhancers	Fetal Heart	heart
17	chr1:216879200-216879400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:216879200-216879400	Bivalent Enhancer	Left Ventricle	heart
19	chr1:216879200-216879600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:216879200-216879600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:216879200-216880000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr1:216879200-216880000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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