Variant report

Variant	rs10064995
Chromosome Location	chr5:146704598-146704599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10054226	1.00[JPT][hapmap]
rs10059609	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10077515	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10477336	0.92[ASW][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes]
rs11741401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747533	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11954258	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11955126	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12054990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364371	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1424293	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs17547843	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17548011	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1834122	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs62377743	0.92[ASN][1000 genomes]
rs6872292	0.90[YRI][hapmap];0.92[AFR][1000 genomes]
rs6891535	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7707452	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs7710326	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10064995	SH3TC2	cis	cerebellum	SCAN
rs10064995	TNIP1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146688800-146707200	Weak transcription	Pancreas	Pancrea
2	chr5:146703200-146711800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:146703600-146716400	Weak transcription	Ovary	ovary
4	chr5:146703800-146707200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:146703800-146711400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:146704000-146705000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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