Variant report

Variant	rs12488393
Chromosome Location	chr3:191008201-191008202
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:66)

rs_ID	r²[population]
rs10937468	0.85[JPT][hapmap]
rs10937470	0.85[JPT][hapmap]
rs10937471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937472	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937473	0.99[ASN][1000 genomes]
rs10937474	0.99[ASN][1000 genomes]
rs10937475	0.95[ASN][1000 genomes]
rs11711123	0.89[EUR][1000 genomes]
rs11720878	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720880	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1195560	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1195561	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486272	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490850	0.99[ASN][1000 genomes]
rs12495011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495014	0.99[ASN][1000 genomes]
rs12496729	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629952	0.90[EUR][1000 genomes]
rs12631157	0.99[ASN][1000 genomes]
rs12638308	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638950	0.98[ASN][1000 genomes]
rs13062195	0.90[EUR][1000 genomes]
rs13067368	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078168	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369280	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398717	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398718	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435064	0.95[ASN][1000 genomes]
rs1435065	0.98[ASN][1000 genomes]
rs1435066	0.98[ASN][1000 genomes]
rs150503	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584934	0.88[EUR][1000 genomes]
rs1584935	0.99[ASN][1000 genomes]
rs1594950	0.99[ASN][1000 genomes]
rs184142	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2117544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117545	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2117546	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117547	0.99[ASN][1000 genomes]
rs2572061	0.90[ASN][1000 genomes]
rs293862	0.82[EUR][1000 genomes]
rs293863	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs293866	0.93[ASN][1000 genomes]
rs293867	0.92[ASN][1000 genomes]
rs34670047	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34848591	0.83[EUR][1000 genomes]
rs55661359	0.94[ASN][1000 genomes]
rs6444533	0.85[JPT][hapmap]
rs66501888	0.88[EUR][1000 genomes]
rs6765280	0.99[ASN][1000 genomes]
rs6765783	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769894	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6769898	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769915	0.99[ASN][1000 genomes]
rs67775561	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6786046	0.99[ASN][1000 genomes]
rs6788097	0.85[JPT][hapmap]
rs6788319	0.85[JPT][hapmap]
rs6794234	0.99[ASN][1000 genomes]
rs6796119	0.95[ASN][1000 genomes]
rs6801672	0.98[ASN][1000 genomes]
rs6801766	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802677	0.81[JPT][hapmap]
rs7645540	0.85[JPT][hapmap]
rs9835846	0.99[ASN][1000 genomes]
rs9854723	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv997716	chr3:190943706-191027499	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv10369	chr3:190994774-191011447	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12488393	LEPREL1	cis	parietal	SCAN
rs12488393	LPP	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191008000-191008600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:191008000-191008600	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:191008000-191009000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr3:191008000-191009200	Flanking Active TSS	GM12878-XiMat	blood
5	chr3:191008200-191008400	Enhancers	Right Atrium	heart
6	chr3:191008200-191008400	Enhancers	Osteobl	bone
7	chr3:191008200-191008600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:191008200-191008600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:191008200-191008600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:191008200-191008600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:191008200-191008600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:191008200-191008600	Flanking Active TSS	NHDF-Ad	bronchial
13	chr3:191008200-191008800	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:191008200-191009000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:191008200-191009000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:191008200-191009000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:191008200-191009200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:191008200-191009800	Enhancers	Primary monocytes fromperipheralblood	blood

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