Variant report

Variant	rs6016705
Chromosome Location	chr20:40802247-40802248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1014757	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11907691	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11907769	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12625238	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13040788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16986670	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1883376	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1883377	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1883378	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1984399	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2143008	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2143632	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2179336	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2206168	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2206169	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2223425	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2223426	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223718	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2867061	0.80[CHD][hapmap]
rs2867062	0.80[CHD][hapmap]
rs2867063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2903465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140521	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4331574	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4375930	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4425144	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6016706	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6016707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6016708	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6016709	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6016710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6016711	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6016712	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6016713	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6016716	0.89[ASN][1000 genomes]
rs6016722	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6016726	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6030011	0.80[EUR][1000 genomes]
rs6030018	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6030023	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6030026	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6030027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6030029	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6030033	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6030035	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6030036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6030037	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6030056	0.80[ASN][1000 genomes]
rs6030058	0.90[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6030061	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6030070	0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs6030071	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6030072	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6030073	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6030076	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs6030082	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6030083	0.81[ASN][1000 genomes]
rs6030084	0.81[JPT][hapmap]
rs6030085	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs6030087	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6030088	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6030089	0.81[CHB][hapmap]
rs6030096	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs6030100	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6065450	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6072651	0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6093584	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6093588	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6093589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6093595	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6093598	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6102704	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6102713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6102714	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6124427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6124429	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6130062	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs6130068	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6130071	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6130073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6130074	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6130076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6130081	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6513772	0.86[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7270492	0.84[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs727337	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs728373	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs728374	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs742290	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs742291	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs926647	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs932358	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs979634	0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[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	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6016705	SPINLW1	cis	parietal	SCAN
rs6016705	CTNNBL1	cis	cerebellum	SCAN
rs6016705	ADA	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40796400-40803600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:40800800-40802600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr20:40801600-40802400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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