Variant report

Variant	rs1895068
Chromosome Location	chr3:177693513-177693514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1075544	1.00[ASN][1000 genomes]
rs10936960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919677	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs11920776	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11922170	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12489750	0.80[ASN][1000 genomes]
rs12492409	0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12495203	0.85[ASN][1000 genomes]
rs12496207	0.86[ASN][1000 genomes]
rs12497387	0.82[ASN][1000 genomes]
rs13062823	0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs13066104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075342	0.82[ASN][1000 genomes]
rs13087011	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13314585	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1362828	0.89[ASN][1000 genomes]
rs1362829	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421157	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421160	0.97[ASN][1000 genomes]
rs1421161	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421166	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421167	0.96[ASN][1000 genomes]
rs1421170	0.90[ASN][1000 genomes]
rs1421173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16828811	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16828819	0.81[ASN][1000 genomes]
rs1895072	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1895073	0.88[ASN][1000 genomes]
rs1895074	0.89[ASN][1000 genomes]
rs1895075	0.86[ASN][1000 genomes]
rs2160836	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34300091	0.90[ASN][1000 genomes]
rs34534264	0.80[ASN][1000 genomes]
rs35751119	0.84[ASN][1000 genomes]
rs3961634	0.89[ASN][1000 genomes]
rs3978728	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs57315928	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775561	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6775970	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776256	0.86[ASN][1000 genomes]
rs6779965	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6783796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6786110	0.84[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6787124	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6804905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737553	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737555	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7619802	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7645977	0.99[ASN][1000 genomes]
rs7648771	0.82[ASN][1000 genomes]
rs9830203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838142	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv829805	chr3:177662113-177805003	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv997975	chr3:177664921-177719623	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1895068	ATP11B	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177691400-177694400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:177691400-177695600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:177691400-177695600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:177691600-177694200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:177691600-177694200	Weak transcription	NHLF	lung
6	chr3:177691600-177694600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:177691600-177695400	Weak transcription	HMEC	breast
8	chr3:177691600-177695400	Weak transcription	NHEK	skin
9	chr3:177691600-177695600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:177691800-177694200	Weak transcription	NHDF-Ad	bronchial
11	chr3:177691800-177694400	Weak transcription	NH-A	brain
12	chr3:177691800-177694600	Weak transcription	A549	lung
13	chr3:177691800-177694600	Weak transcription	HSMM	muscle
14	chr3:177691800-177695200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:177691800-177695400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:177692000-177694400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:177692000-177694400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:177692200-177694200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:177692200-177694200	Weak transcription	Osteobl	bone

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