Variant report

Variant	rs538385
Chromosome Location	chr13:30229665-30229666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTUS2-3	chr13:30229088-30229714	NONHSAT032746

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1104261	0.86[AFR][1000 genomes]
rs2089944	0.90[AFR][1000 genomes]
rs2263207	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2669028	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2776418	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2776951	0.80[AFR][1000 genomes]
rs280905	0.98[ASN][1000 genomes]
rs280906	0.92[ASN][1000 genomes]
rs280907	0.99[ASN][1000 genomes]
rs280908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs280941	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs280942	0.81[ASN][1000 genomes]
rs280943	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs280944	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs280945	0.81[ASN][1000 genomes]
rs482876	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs489679	0.99[ASN][1000 genomes]
rs517178	0.83[ASN][1000 genomes]
rs524368	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs529739	0.99[ASN][1000 genomes]
rs535141	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs550984	0.99[ASN][1000 genomes]
rs563630	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs565279	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs566736	0.81[ASN][1000 genomes]
rs570095	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs571899	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs573080	0.86[AFR][1000 genomes]
rs590377	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs606753	0.82[ASN][1000 genomes]
rs61947189	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs630273	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648326	0.99[ASN][1000 genomes]
rs819400	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs819401	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs819406	0.90[AFR][1000 genomes]
rs819408	0.88[AFR][1000 genomes]
rs9506213	0.92[ASN][1000 genomes]
rs9506214	0.92[ASN][1000 genomes]
rs9506215	0.92[ASN][1000 genomes]
rs9508524	0.86[ASN][1000 genomes]
rs9551713	0.92[ASN][1000 genomes]
rs9551714	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[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	nsv980	chr13:30200197-30236915	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv510577	chr13:30213612-30254316	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs538385	SLC7A1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30222800-30232800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr13:30222800-30232800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:30228000-30230000	Enhancers	NHLF	lung
4	chr13:30228000-30230000	Enhancers	Osteobl	bone
5	chr13:30228000-30230600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:30228200-30230000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:30228200-30230000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:30228400-30233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:30229000-30229800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr13:30229200-30229800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:30229200-30229800	Flanking Active TSS	NHDF-Ad	bronchial
12	chr13:30229200-30230000	Enhancers	HSMM	muscle
13	chr13:30229200-30230000	Enhancers	NH-A	brain
14	chr13:30229400-30230000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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