Variant report

Variant	rs874808
Chromosome Location	chr6:38773293-38773294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38771295..38773391-chr6:38780024..38781597,2	K562	blood:
2	chr6:38767591..38769178-chr6:38771551..38774399,2	K562	blood:
3	chr6:38761644..38764833-chr6:38770187..38773339,3	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1018437	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1564377	0.81[EUR][1000 genomes]
rs1622275	0.92[ASW][hapmap];0.88[YRI][hapmap]
rs1629877	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678681	0.80[YRI][hapmap]
rs1678682	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678686	0.83[YRI][hapmap]
rs1678688	0.88[YRI][hapmap]
rs1678690	1.00[CEU][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1678691	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1678692	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1678693	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1678694	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678695	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678696	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678697	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678698	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678699	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678700	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678701	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678702	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678703	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1678706	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678707	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678708	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678709	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678712	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678717	0.96[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs1678742	0.92[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1738199	0.88[EUR][1000 genomes]
rs1738203	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1738211	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1738212	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1738215	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1738216	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1738217	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1738218	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1738219	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1738220	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1738221	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1738223	0.88[YRI][hapmap]
rs1738225	0.85[ASW][hapmap]
rs1738226	0.93[ASW][hapmap];0.88[YRI][hapmap]
rs1738227	0.93[ASW][hapmap];0.88[YRI][hapmap]
rs1738228	0.80[YRI][hapmap]
rs1738229	0.93[ASW][hapmap];0.88[YRI][hapmap]
rs1738230	0.87[YRI][hapmap]
rs1738231	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1738241	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2061907	0.92[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2179711	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2179712	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2179713	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2395709	0.92[CEU][hapmap]
rs4302660	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs4380739	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs4386804	0.92[CEU][hapmap]
rs4391252	0.92[CEU][hapmap]
rs4443498	0.92[CEU][hapmap]
rs4501424	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4571559	0.88[CEU][hapmap]
rs4590258	0.92[CEU][hapmap]
rs4711558	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4714193	0.92[CEU][hapmap]
rs6458073	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs6458074	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6458075	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6458076	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6458077	0.81[EUR][1000 genomes]
rs6458078	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6458080	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs6458081	0.92[CEU][hapmap]
rs6912563	0.87[YRI][hapmap]
rs6919465	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6928952	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6931736	0.92[CEU][hapmap]
rs6934064	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs726108	0.88[YRI][hapmap]
rs7748684	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs7772148	0.82[EUR][1000 genomes]
rs9296265	0.92[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9349100	0.82[EUR][1000 genomes]
rs9357290	0.92[CEU][hapmap]
rs9366982	0.92[CEU][hapmap]
rs9369085	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9369087	0.82[EUR][1000 genomes]
rs9369088	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs9369089	0.92[CEU][hapmap]
rs9380789	0.88[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9380791	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs9380792	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs9380796	0.92[CEU][hapmap]
rs9380798	0.92[CEU][hapmap]
rs9380799	0.92[CEU][hapmap]
rs9394545	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs9394547	0.92[CEU][hapmap]
rs9394549	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs9394550	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs984523	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs984524	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs984525	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	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	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
3	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
4	nsv462915	chr6:38728142-38773293	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602959	chr6:38728142-38786528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv470814	chr6:38728142-38790149	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv462916	chr6:38747770-38782401	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv602960	chr6:38747770-38782401	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs874808	TREM2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38766800-38824400	Weak transcription	K562	blood
2	chr6:38769800-38773600	Weak transcription	GM12878-XiMat	blood
3	chr6:38772000-38775200	Enhancers	HUVEC	blood vessel
4	chr6:38772600-38773800	Weak transcription	Fetal Muscle Leg	muscle

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