Variant report

Variant	rs13397044
Chromosome Location	chr2:77284280-77284281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10186823	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12713890	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs13021476	0.85[CEU][hapmap]
rs13033902	0.89[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap]
rs13034088	0.89[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs13430336	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1348825	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1348828	0.84[CEU][hapmap]
rs1374392	0.85[CEU][hapmap]
rs1374394	0.94[GIH][hapmap]
rs1446689	1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs1446690	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1446694	0.84[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs1446706	0.84[CEU][hapmap]
rs1446717	0.85[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap]
rs1446718	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs1446720	0.84[CEU][hapmap]
rs1542187	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs17013615	0.84[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap]
rs17040496	0.85[CEU][hapmap]
rs17040500	0.84[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap]
rs17089	0.84[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap]
rs1867891	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1900342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982341	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4510248	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs4853290	0.84[CEU][hapmap]
rs6547106	0.83[GIH][hapmap]
rs6547107	0.85[CEU][hapmap]
rs6547108	0.85[CEU][hapmap]
rs6547109	0.85[CEU][hapmap]
rs6547111	0.85[CEU][hapmap]
rs6547113	0.84[CEU][hapmap]
rs6547119	0.90[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs6737296	0.85[CEU][hapmap]
rs6754347	0.94[CEU][hapmap]
rs6758707	0.83[CEU][hapmap]
rs7561189	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs7595678	0.84[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834266	chr2:77120236-77287504	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv997284	chr2:77233426-77303198	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1014895	chr2:77263452-77414507	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv874331	chr2:77264354-77305123	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv458285	chr2:77276201-77345491	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
7	nsv582252	chr2:77276201-77345491	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13397044	SMYD5	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77278800-77286400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:77280800-77286200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:77281600-77286600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:77282400-77286800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:77284200-77284600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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