Variant report

Variant	rs1869859
Chromosome Location	chr3:157107762-157107763
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1027603	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10936085	0.88[CHB][hapmap]
rs10936086	0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10936087	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486427	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12492874	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12492929	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12496879	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs12629552	0.82[EUR][1000 genomes]
rs12636038	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12638732	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13087207	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1456097	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1456105	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456106	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456110	0.83[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1500916	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1500919	0.83[EUR][1000 genomes]
rs1500920	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1545596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546261	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1563420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568609	0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs1585080	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1824058	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[EUR][1000 genomes]
rs1840668	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1840673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869857	0.84[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1965246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047649	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2085315	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305620	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305622	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28638274	0.84[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs35004310	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3816527	0.83[CHB][hapmap]
rs3816528	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4435581	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4482625	0.82[EUR][1000 genomes]
rs4640512	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4640513	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4679793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680358	0.83[EUR][1000 genomes]
rs4680359	0.88[CHB][hapmap]
rs4680360	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs56249701	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6441126	0.88[CHB][hapmap];0.82[JPT][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441127	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6441128	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441129	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6801110	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6803628	0.88[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs722484	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7614339	0.83[CEU][hapmap];0.80[CHB][hapmap]
rs7617727	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618502	0.82[EUR][1000 genomes]
rs7618737	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7623173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629293	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631556	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7639254	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9857875	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs9871290	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9878474	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9883103	0.89[CHB][hapmap]
rs988587	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs988588	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9990136	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.83[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1869859	SSR3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157088000-157108600	Weak transcription	Lung	lung
2	chr3:157091800-157108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:157091800-157142600	Weak transcription	Pancreas	Pancrea
4	chr3:157104000-157108400	Weak transcription	Aorta	Aorta
5	chr3:157104600-157108600	Weak transcription	Ovary	ovary
6	chr3:157105200-157109200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:157105400-157107800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:157105400-157108000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:157106000-157108000	Enhancers	HUVEC	blood vessel
10	chr3:157106200-157107800	Enhancers	NHLF	lung
11	chr3:157106400-157108600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:157106400-157108600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:157106800-157108600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:157107200-157108400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:157107200-157108600	Weak transcription	NHEK	skin
16	chr3:157107200-157109000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:157107200-157111000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:157107200-157119000	Weak transcription	Fetal Lung	lung
19	chr3:157107400-157108400	Weak transcription	NHDF-Ad	bronchial
20	chr3:157107400-157108600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:157107400-157109000	Weak transcription	Osteobl	bone
22	chr3:157107400-157128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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