Variant report

Variant	rs9380804
Chromosome Location	chr6:38852719-38852720
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	chr6:38851556..38854549-chr6:38855510..38859290,4	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1564378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[ASN][1000 genomes]
rs1678694	0.81[CHB][hapmap]
rs1678698	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap]
rs1678699	0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap]
rs1678703	0.81[CHB][hapmap]
rs1678708	0.81[CHB][hapmap]
rs1678709	0.81[CHB][hapmap]
rs1738211	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap]
rs1738215	0.81[CHB][hapmap]
rs2061907	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap]
rs2179711	0.85[CHB][hapmap]
rs2179712	0.85[CHB][hapmap]
rs2179713	0.85[CHB][hapmap]
rs4302660	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[ASN][1000 genomes]
rs4501424	0.85[CHB][hapmap]
rs4711560	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs6458073	0.83[CHB][hapmap]
rs6458074	0.85[CHB][hapmap]
rs6458075	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap]
rs6458076	0.89[CHB][hapmap]
rs6458078	0.85[CHB][hapmap]
rs6928952	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs6934064	0.85[CHB][hapmap]
rs7748684	0.85[CHB][hapmap]
rs9369085	0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap]
rs9369088	0.85[CHB][hapmap]
rs9380791	0.81[GIH][hapmap]
rs9380792	0.87[CHB][hapmap]
rs9380802	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9394543	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs9394545	0.85[CHB][hapmap]
rs9394549	0.85[CHB][hapmap]
rs984525	0.81[CHB][hapmap]

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	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
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9380804	LRFN2	cis	cerebellum	SCAN
rs9380804	GLO1	cis	lymphoblastoid	seeQTL
rs9380804	TREM2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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