Variant report

Variant	rs9819258
Chromosome Location	chr3:59879030-59879031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11915344	0.83[ASN][1000 genomes]
rs11920587	0.83[ASN][1000 genomes]
rs11924342	1.00[CHD][hapmap]
rs17061340	0.83[ASN][1000 genomes]
rs17061346	0.83[ASN][1000 genomes]
rs17061373	0.83[ASN][1000 genomes]
rs17061385	0.83[ASN][1000 genomes]
rs17061388	1.00[CHD][hapmap]
rs17061428	0.83[ASN][1000 genomes]
rs17299801	1.00[CHD][hapmap]
rs294451	0.81[CEU][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56122642	0.83[ASN][1000 genomes]
rs56838688	0.83[ASN][1000 genomes]
rs59843181	0.83[ASN][1000 genomes]
rs602197	0.83[CEU][hapmap]
rs604398	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6446087	0.87[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs687069	1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73839568	0.83[ASN][1000 genomes]
rs73839569	0.83[ASN][1000 genomes]
rs73839584	0.83[ASN][1000 genomes]
rs73839586	0.83[ASN][1000 genomes]
rs73839587	0.83[ASN][1000 genomes]
rs73839592	0.83[ASN][1000 genomes]
rs73839594	0.83[ASN][1000 genomes]
rs73839596	0.83[ASN][1000 genomes]
rs750793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs780712	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9284900	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9311738	1.00[CHD][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs9311739	0.93[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9844365	0.83[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9851655	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9851805	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9851914	0.87[AMR][1000 genomes]
rs9853482	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9868156	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9871827	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590386	chr3:59846067-59912377	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1002104	chr3:59875996-59907597	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9819258	SPATA12	cis	parietal	SCAN
rs9819258	MOB2	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59868800-59882600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:59871400-59879200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:59872600-59880600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:59872600-59880600	Weak transcription	Fetal Thymus	thymus
5	chr3:59872600-59884200	Weak transcription	Dnd41	blood
6	chr3:59873200-59904200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:59875200-59880400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:59877200-59880200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:59877200-59880400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:59877800-59880600	Weak transcription	Primary T cells from cord blood	blood

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