Variant report

Variant	rs6901086
Chromosome Location	chr6:38430409-38430410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12191714	1.00[JPT][hapmap]
rs12206324	1.00[JPT][hapmap]
rs12206905	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12212983	1.00[JPT][hapmap]
rs12215850	1.00[JPT][hapmap]
rs1883610	0.86[JPT][hapmap]
rs1983605	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs28445226	1.00[JPT][hapmap]
rs4236058	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4711542	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4711546	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4714148	0.88[CHD][hapmap]
rs4714152	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4714157	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714161	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714164	0.85[ASN][1000 genomes]
rs4714165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60936387	0.86[ASN][1000 genomes]
rs61192259	0.86[ASN][1000 genomes]
rs6458054	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909898	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6933268	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs6933758	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6940319	1.00[JPT][hapmap]
rs742515	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7748599	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7749685	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7759629	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7766214	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7770868	0.88[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs871183	1.00[JPT][hapmap]
rs9349073	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9357272	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9380743	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9394492	0.88[CHD][hapmap]
rs9394495	1.00[JPT][hapmap]
rs9394500	0.85[ASN][1000 genomes]
rs9470885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470888	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs9470891	0.88[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6901086	TREM2	cis	cerebellum	SCAN
rs6901086	BYSL	cis	parietal	SCAN
rs6901086	GLO1	cis	cerebellum	SCAN
rs6901086	GLO1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:38412200-38445600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:38414000-38438400	Weak transcription	Left Ventricle	heart
4	chr6:38414800-38432200	Weak transcription	Aorta	Aorta
5	chr6:38425200-38438400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:38427600-38437200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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