Variant report

Variant	rs9395084
Chromosome Location	chr6:45220175-45220176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10948222	0.92[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs12199720	0.92[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs12205312	0.81[EUR][1000 genomes]
rs12207402	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1321081	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs1555681	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17209755	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2093901	0.83[EUR][1000 genomes]
rs2093903	0.83[EUR][1000 genomes]
rs2396425	0.89[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs3749863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs3923353	0.87[EUR][1000 genomes]
rs4373351	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4446571	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4506035	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4510673	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs4631280	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458419	0.89[CEU][hapmap]
rs6458428	0.84[EUR][1000 genomes]
rs6899845	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs6934594	0.89[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs6935398	0.87[EUR][1000 genomes]
rs6937317	0.89[EUR][1000 genomes]
rs7451423	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs7740083	0.83[EUR][1000 genomes]
rs7770401	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9296453	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs9296457	0.83[EUR][1000 genomes]
rs9349315	0.85[EUR][1000 genomes]
rs9357469	0.89[CEU][hapmap]
rs9357471	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9357478	0.84[EUR][1000 genomes]
rs9357480	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs9357484	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs9369552	0.90[EUR][1000 genomes]
rs9369558	0.92[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9381377	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381383	0.82[EUR][1000 genomes]
rs9395066	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs9395069	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9395086	0.91[EUR][1000 genomes]
rs9395087	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395095	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9463078	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463081	0.84[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs9463083	0.81[EUR][1000 genomes]
rs9472460	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9472487	0.82[ASW][hapmap];1.00[LWK][hapmap]

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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv492309	chr6:45020402-45233484	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1028068	chr6:45169010-45246577	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2763550	chr6:45186825-45275593	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv830652	chr6:45187467-45328983	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9395084	SUPT3H	cis	multi-tissue	Pritchard
rs9395084	MAD2L1BP	cis	cerebellum	SCAN
rs9395084	C6orf226	cis	cerebellum	SCAN
rs9395084	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs9395084	CD2AP	cis	parietal	SCAN
rs9395084	SUPT3H	cis	cerebellum	SCAN
rs9395084	SUPT3H	cis	lymphoblastoid	seeQTL
rs9395084	SUPT3H	cis	parietal	SCAN
rs9395084	CYP39A1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45211400-45220200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:45213800-45221200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:45218600-45239000	Weak transcription	Dnd41	blood

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