Variant report

Variant	rs1537231
Chromosome Location	chr6:38947835-38947836
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10947766	0.96[CHD][hapmap]
rs10947767	0.96[CHD][hapmap]
rs11753074	0.81[CEU][hapmap]
rs11753138	0.81[CEU][hapmap]
rs12203833	0.96[CHD][hapmap]
rs1332012	0.90[CEU][hapmap]
rs1332014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332015	1.00[JPT][hapmap]
rs16891340	0.96[CHD][hapmap]
rs2150891	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2235871	1.00[CEU][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273093	1.00[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2281340	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281346	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395710	0.90[CEU][hapmap]
rs2894418	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3857575	0.81[CEU][hapmap]
rs4714202	0.90[CEU][hapmap]
rs4714203	0.90[CEU][hapmap]
rs4714204	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4714208	1.00[CEU][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs506672	0.90[CEU][hapmap]
rs6458088	0.90[CEU][hapmap]
rs761384	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761385	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7766930	1.00[CEU][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs926674	1.00[ASW][hapmap]
rs9296273	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9357295	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366992	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9369100	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9380815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380817	1.00[CEU][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs9380818	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9462460	0.81[CEU][hapmap]
rs9462464	0.81[CEU][hapmap]
rs9462466	0.81[CEU][hapmap]
rs9462469	1.00[CEU][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470949	0.81[CEU][hapmap]
rs9470950	0.81[CEU][hapmap]
rs9470961	0.80[CEU][hapmap]
rs9470962	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	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	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
3	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
4	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
5	nsv948357	chr6:38920998-39035836	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1537231	TREM2	cis	parietal	SCAN
rs1537231	PPIL1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38945000-38950000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:38945200-38949800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:38945200-38950000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:38945200-38950200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:38945200-38950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:38945200-38958400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:38945400-38958000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:38945600-38950200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:38945800-38950000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:38946200-38952400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:38947000-38950200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:38947000-38950200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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