Variant report

Variant	rs1870709
Chromosome Location	chr3:115952799-115952800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10934323	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934326	0.82[EUR][1000 genomes]
rs11719629	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11920943	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs12492442	0.83[CHB][hapmap]
rs12494106	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496133	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634800	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12695324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13095238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381068	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1381070	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1431512	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1461121	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1461125	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1461126	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544994	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1549831	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549832	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16824649	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824686	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16824691	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs16824693	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16824696	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16845196	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs1870707	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1870708	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1993732	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279109	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306064	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2867101	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867102	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903483	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3195	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34500521	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147304	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4831090	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4831125	0.81[ASN][1000 genomes]
rs4831126	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4831127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4831128	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4831129	0.80[CHD][hapmap]
rs61254748	0.83[EUR][1000 genomes]
rs6438308	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438310	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6765043	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778040	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805045	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73141002	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73143006	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73143010	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73861405	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7426468	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7431707	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7624352	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637684	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642172	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7645796	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7653282	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289048	0.80[ASN][1000 genomes]
rs9826213	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9828943	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9830749	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9835427	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836892	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850908	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866532	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9866706	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874470	0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs9875017	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv877360	chr3:115916171-116023990	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	esv1808373	chr3:115952799-115984473	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1870709	ZDHHC23	cis	cerebellum	SCAN
rs1870709	UPK1B	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115949600-115952800	Weak transcription	Brain Substantia Nigra	brain
2	chr3:115949600-115952800	Weak transcription	Fetal Kidney	kidney
3	chr3:115949600-115956200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:115949600-115965400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:115951200-115955400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:115952400-115953200	Enhancers	Colon Smooth Muscle	Colon
7	chr3:115952600-115953200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:115952600-115953200	Enhancers	Brain Angular Gyrus	brain
9	chr3:115952600-115953200	Enhancers	Brain Anterior Caudate	brain
10	chr3:115952600-115953200	Enhancers	Brain Inferior Temporal Lobe	brain

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