Variant report

Variant	rs9369085
Chromosome Location	chr6:38820451-38820452
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	chr6:38819628..38821796-chr6:38823200..38825127,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1008227	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1018437	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs1564377	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564378	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs1629877	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678682	0.83[EUR][1000 genomes]
rs1678690	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1678691	0.85[EUR][1000 genomes]
rs1678692	0.85[EUR][1000 genomes]
rs1678693	0.86[EUR][1000 genomes]
rs1678694	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1678695	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678696	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678697	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678698	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678699	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678700	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678701	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678702	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678703	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678706	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678707	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678708	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678709	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1678712	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678717	0.96[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1678742	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1738199	0.93[EUR][1000 genomes]
rs1738203	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1738211	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738212	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738215	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738216	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738217	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738218	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738219	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1738220	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs1738221	0.86[EUR][1000 genomes]
rs1738231	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1738241	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2061907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2395709	1.00[CEU][hapmap]
rs35696175	0.83[EUR][1000 genomes]
rs4302660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4380739	1.00[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4386804	1.00[CEU][hapmap]
rs4391252	1.00[CEU][hapmap]
rs4443498	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4501424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4571559	0.96[CEU][hapmap]
rs4590258	1.00[CEU][hapmap]
rs4711558	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4711559	0.82[EUR][1000 genomes]
rs4714193	1.00[CEU][hapmap]
rs6458073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458077	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458079	0.83[EUR][1000 genomes]
rs6458080	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6458081	1.00[CEU][hapmap]
rs6919465	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6928952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6931736	1.00[CEU][hapmap]
rs6934064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7746153	0.83[EUR][1000 genomes]
rs7748684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757460	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7772148	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874808	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]
rs9296265	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9349100	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9357290	1.00[CEU][hapmap]
rs9366982	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9369087	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9369088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9369089	1.00[CEU][hapmap]
rs9380787	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9380788	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9380789	0.92[ASW][hapmap];0.96[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9380791	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs9380792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9380795	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9380796	1.00[CEU][hapmap]
rs9380798	1.00[CEU][hapmap]
rs9380799	1.00[CEU][hapmap]
rs9380804	0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap]
rs9394544	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9394545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394547	1.00[CEU][hapmap]
rs9394549	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9394550	1.00[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs984523	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs984524	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs984525	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9369085	TREM2	cis	parietal	SCAN
rs9369085	BTBD9	cis	cerebellum	SCAN
rs9369085	LRFN2	cis	parietal	SCAN

Chromatin state (count:7 , 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	chr6:38819600-38820600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr6:38819800-38821200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:38820000-38820800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:38820000-38821000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links