Variant report

Variant	rs1678742
Chromosome Location	chr6:38815827-38815828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38813265..38816025-chr6:38831450..38834352,2	K562	blood:

Variant related genes	Relation type
ENSG00000124721	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1008227	0.92[EUR][1000 genomes]
rs1018437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1157884	1.00[JPT][hapmap]
rs1564377	0.96[EUR][1000 genomes]
rs1614699	0.93[JPT][hapmap]
rs1629877	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678638	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1678640	0.93[ASN][1000 genomes]
rs1678657	0.93[JPT][hapmap]
rs1678669	1.00[JPT][hapmap]
rs1678675	0.92[JPT][hapmap]
rs1678682	0.84[EUR][1000 genomes]
rs1678690	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1678691	0.87[EUR][1000 genomes]
rs1678692	0.87[EUR][1000 genomes]
rs1678693	0.88[EUR][1000 genomes]
rs1678694	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1678695	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678696	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678697	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678698	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678699	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678700	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678701	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678702	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678703	0.96[CEU][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1678706	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678707	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678708	0.96[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678709	0.96[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678712	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1678717	0.83[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678718	0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1678725	0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1678727	0.82[ASN][1000 genomes]
rs1738177	0.80[JPT][hapmap]
rs1738184	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1738192	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1738199	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1738203	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1738211	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1738212	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1738215	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1738216	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1738217	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1738218	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1738219	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1738220	0.92[CEU][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs1738221	0.88[EUR][1000 genomes]
rs1738231	0.91[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs1738239	1.00[JPT][hapmap]
rs1738240	0.93[JPT][hapmap]
rs1738241	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1738243	1.00[JPT][hapmap]
rs1738247	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1738263	0.93[JPT][hapmap]
rs2061907	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2179711	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2179712	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2179713	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2395709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2746170	0.80[JPT][hapmap]
rs35696175	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4286777	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4302660	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4380739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4386804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4391252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4443498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4501424	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4571559	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4590258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711559	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711560	0.87[CHD][hapmap];0.93[GIH][hapmap]
rs4714193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6458073	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6458074	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6458075	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6458076	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6458077	0.94[EUR][1000 genomes]
rs6458078	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6458079	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6919465	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6928952	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6931736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6934064	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs769064	0.80[JPT][hapmap]
rs7746153	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7748684	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7757460	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7772148	0.97[EUR][1000 genomes]
rs862422	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs862425	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs862427	0.80[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs862438	1.00[CHB][hapmap]
rs874808	0.92[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9296265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296268	1.00[CHB][hapmap]
rs9349100	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs9366982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9369085	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs9369087	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369088	1.00[CEU][hapmap]
rs9369089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9380787	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380788	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380789	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs9380792	1.00[CEU][hapmap]
rs9380795	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9380798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9380799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9394531	0.80[JPT][hapmap]
rs9394544	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394545	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9394547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9394549	0.87[CEU][hapmap]
rs9394550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs982705	0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs984524	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs984525	0.96[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1678742	TREM2	cis	parietal	SCAN
rs1678742	LRFN2	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	chr6:38804600-38821000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:38812600-38821000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:38814400-38816800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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