Variant report

Variant	rs9357280
Chromosome Location	chr6:38723575-38723576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38713215..38715791-chr6:38723415..38725605,2	K562	blood:
2	chr6:38722850..38724981-chr6:38761101..38763461,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12173602	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1612377	0.90[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1615744	0.89[ASN][1000 genomes]
rs1678639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1678642	0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1678643	0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1678652	0.85[ASN][1000 genomes]
rs1678653	0.85[ASN][1000 genomes]
rs1678654	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678655	0.85[ASN][1000 genomes]
rs1678656	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678658	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678659	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678662	0.85[ASN][1000 genomes]
rs1678663	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678664	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1678672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678677	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1678678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678679	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678684	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1678736	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738174	0.87[ASN][1000 genomes]
rs1738175	0.88[ASN][1000 genomes]
rs1738176	0.89[ASN][1000 genomes]
rs1738178	0.89[ASN][1000 genomes]
rs1738179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738180	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738181	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738182	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738183	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1738251	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1738252	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738253	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738254	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738255	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738256	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738259	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1738260	0.91[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1738261	0.85[ASN][1000 genomes]
rs1738262	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738264	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1738265	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738266	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1738267	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738268	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738269	0.87[ASN][1000 genomes]
rs2448400	0.91[ASN][1000 genomes]
rs2448401	0.91[ASN][1000 genomes]
rs4714178	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58817640	0.86[ASN][1000 genomes]
rs9394532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9357280	SYPL2	trans	lymphoblastoid	seeQTL
rs9357280	DNAH8	cis	multi-tissue	Pritchard
rs9357280	EIF4EBP1	trans	lymphoblastoid	seeQTL
rs9357280	XKR4	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38706200-38738600	Weak transcription	K562	blood
2	chr6:38722400-38724200	Enhancers	HMEC	breast
3	chr6:38722400-38724200	Enhancers	NHEK	skin
4	chr6:38722600-38724200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:38722600-38724200	Enhancers	Stomach Mucosa	stomach
6	chr6:38722800-38723800	Enhancers	Fetal Kidney	kidney
7	chr6:38723000-38724200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:38723400-38738400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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