Variant report

Variant	rs9399315
Chromosome Location	chr6:140722426-140722427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs11155107	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1119397	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs1121833	0.86[ASN][1000 genomes]
rs12055615	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12174980	0.81[ASN][1000 genomes]
rs12660474	0.83[ASN][1000 genomes]
rs12661752	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662046	0.83[ASN][1000 genomes]
rs12662848	0.86[ASN][1000 genomes]
rs12663424	0.87[ASN][1000 genomes]
rs12663444	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12663480	0.81[ASN][1000 genomes]
rs12665797	0.83[ASN][1000 genomes]
rs13191640	0.81[ASN][1000 genomes]
rs13192756	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194271	0.87[ASN][1000 genomes]
rs13204703	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13207048	0.81[ASN][1000 genomes]
rs13208097	0.87[ASN][1000 genomes]
rs13210978	0.81[ASN][1000 genomes]
rs13213875	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220827	0.81[ASN][1000 genomes]
rs1336373	0.80[ASN][1000 genomes]
rs1496110	0.83[ASN][1000 genomes]
rs1496112	0.81[ASN][1000 genomes]
rs1496113	0.81[ASN][1000 genomes]
rs1519592	0.81[ASN][1000 genomes]
rs1587171	0.81[ASN][1000 genomes]
rs1603348	0.81[ASN][1000 genomes]
rs1603349	0.81[ASN][1000 genomes]
rs17053906	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17069852	0.81[ASN][1000 genomes]
rs17069854	0.81[ASN][1000 genomes]
rs17069978	0.81[ASN][1000 genomes]
rs17192	0.86[ASN][1000 genomes]
rs1856752	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050135	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2103669	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2328062	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34234462	0.81[ASN][1000 genomes]
rs34753441	0.81[ASN][1000 genomes]
rs34803000	0.81[ASN][1000 genomes]
rs34858573	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34984534	0.81[ASN][1000 genomes]
rs35178101	0.81[ASN][1000 genomes]
rs35465283	0.81[ASN][1000 genomes]
rs35626395	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35686278	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36074095	0.81[ASN][1000 genomes]
rs4323321	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4391280	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4562159	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4637665	0.81[ASN][1000 genomes]
rs477498	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4896508	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896509	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs520322	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs533610	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57291519	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66605907	0.84[ASN][1000 genomes]
rs67956550	0.81[ASN][1000 genomes]
rs9321765	0.83[ASN][1000 genomes]
rs9321769	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9373260	0.81[ASN][1000 genomes]
rs9373261	0.81[ASN][1000 genomes]
rs9373262	0.81[ASN][1000 genomes]
rs9373266	0.83[ASN][1000 genomes]
rs9373267	0.81[ASN][1000 genomes]
rs9373269	0.86[ASN][1000 genomes]
rs9373270	0.86[ASN][1000 genomes]
rs9373272	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373273	0.90[ASN][1000 genomes]
rs9373274	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373276	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9373278	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376502	0.81[ASN][1000 genomes]
rs9376503	0.81[ASN][1000 genomes]
rs9376504	0.81[ASN][1000 genomes]
rs9376506	0.83[ASN][1000 genomes]
rs9376511	0.86[ASN][1000 genomes]
rs9376512	0.86[ASN][1000 genomes]
rs9376518	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385903	0.81[ASN][1000 genomes]
rs9385906	0.81[ASN][1000 genomes]
rs9385908	0.87[ASN][1000 genomes]
rs9389753	0.81[ASN][1000 genomes]
rs9389754	0.81[ASN][1000 genomes]
rs9389755	0.81[ASN][1000 genomes]
rs9389757	0.81[ASN][1000 genomes]
rs9389760	0.81[ASN][1000 genomes]
rs9389763	0.81[ASN][1000 genomes]
rs9389767	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9389768	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9389772	0.83[ASN][1000 genomes]
rs9389773	0.82[ASN][1000 genomes]
rs9389776	0.81[ASN][1000 genomes]
rs9389777	0.81[ASN][1000 genomes]
rs9389780	0.83[ASN][1000 genomes]
rs9389781	0.83[ASN][1000 genomes]
rs9389782	0.82[ASN][1000 genomes]
rs9389783	0.83[ASN][1000 genomes]
rs9389784	0.86[ASN][1000 genomes]
rs9389785	0.86[ASN][1000 genomes]
rs9389789	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9389793	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9389794	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9399310	0.81[ASN][1000 genomes]
rs9399316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403150	0.81[ASN][1000 genomes]
rs9403151	0.81[ASN][1000 genomes]
rs9403153	0.81[ASN][1000 genomes]
rs9403155	0.81[ASN][1000 genomes]
rs9403156	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9403157	0.81[ASN][1000 genomes]
rs9403159	0.81[ASN][1000 genomes]
rs9403168	0.82[ASN][1000 genomes]
rs9403170	0.83[ASN][1000 genomes]
rs9403171	0.86[ASN][1000 genomes]
rs9403173	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9403174	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403176	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403177	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791338	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997388	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015293	chr6:140544956-140798437	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817390	chr6:140558103-141166039	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv432965	chr6:140692307-140866307	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv604767	chr6:140701423-140816108	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv886694	chr6:140701423-141001420	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9399315	HOXB2	trans	lymphoblastoid	seeQTL
rs9399315	CAMK2D	trans	lymphoblastoid	seeQTL
rs9399315	C6orf115	cis	cerebellum	SCAN
rs9399315	HERC5	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140706400-140727000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:140715400-140723000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:140719800-140722600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:140722400-140723400	Enhancers	HMEC	breast

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