Variant report

Variant	rs1569351
Chromosome Location	chr3:60312417-60312418
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1006901	0.85[CEU][hapmap]
rs10510839	0.89[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs11130766	0.92[CEU][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes]
rs12494639	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12498046	1.00[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1546831	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1569350	0.91[ASW][hapmap];0.96[CEU][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1569352	0.81[CHD][hapmap]
rs17599845	0.89[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap]
rs213382	0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs3890406	0.85[CEU][hapmap]
rs6762886	0.96[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs6797780	0.85[CEU][hapmap]
rs6800257	0.88[CEU][hapmap]
rs727476	0.96[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs926143	0.81[CHD][hapmap]
rs9837070	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1009971	chr3:60070974-60397331	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010969	chr3:60124962-60425297	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2422232	chr3:60192201-60334555	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv876844	chr3:60256485-60362565	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv876845	chr3:60256485-60367607	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1001134	chr3:60262617-60344190	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv590394	chr3:60289140-60388900	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv999794	chr3:60301059-60332871	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1011408	chr3:60307954-60417143	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1011133	chr3:60309541-60417339	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv519353	chr3:60310790-60417103	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv460568	chr3:60310790-60417103	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv590395	chr3:60310790-60417103	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1013291	chr3:60312356-60417339	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1569351	SPATA12	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60309400-60321600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:60311200-60313000	Enhancers	Dnd41	blood
3	chr3:60312200-60312800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:60312400-60312600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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