Variant report

Variant	rs5997542
Chromosome Location	chr22:30244719-30244720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12233358	0.89[EUR][1000 genomes]
rs12484010	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484420	1.00[EUR][1000 genomes]
rs12484983	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs13053389	1.00[EUR][1000 genomes]
rs13055998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13057204	0.89[EUR][1000 genomes]
rs13058224	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1476514	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs16988123	1.00[EUR][1000 genomes]
rs16988145	1.00[EUR][1000 genomes]
rs1894472	0.80[AMR][1000 genomes]
rs2010916	0.85[EUR][1000 genomes]
rs2012308	0.89[EUR][1000 genomes]
rs2412961	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs34955393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35361418	0.95[EUR][1000 genomes]
rs35710453	0.89[EUR][1000 genomes]
rs36018230	0.89[EUR][1000 genomes]
rs3788422	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs4343558	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820825	1.00[EUR][1000 genomes]
rs4823054	0.82[GIH][hapmap]
rs4823056	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823058	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823064	1.00[EUR][1000 genomes]
rs4823067	0.89[EUR][1000 genomes]
rs55686007	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5752960	0.85[GIH][hapmap];0.82[MEX][hapmap]
rs5752969	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752976	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752997	1.00[EUR][1000 genomes]
rs5753002	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs5763543	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763544	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763552	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763553	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763556	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763557	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763561	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763566	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763569	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763575	0.80[ASN][1000 genomes]
rs5763585	1.00[EUR][1000 genomes]
rs5763601	1.00[EUR][1000 genomes]
rs5763602	1.00[EUR][1000 genomes]
rs5763604	1.00[EUR][1000 genomes]
rs5763606	1.00[EUR][1000 genomes]
rs5763609	1.00[EUR][1000 genomes]
rs5763629	1.00[EUR][1000 genomes]
rs5763637	1.00[EUR][1000 genomes]
rs5763648	1.00[EUR][1000 genomes]
rs5763662	1.00[EUR][1000 genomes]
rs5763681	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs5763687	1.00[EUR][1000 genomes]
rs5763695	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs5763701	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs5763734	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs5763742	0.89[EUR][1000 genomes]
rs5763746	0.89[EUR][1000 genomes]
rs5763748	0.89[EUR][1000 genomes]
rs5763750	0.89[EUR][1000 genomes]
rs6006278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71331220	1.00[EUR][1000 genomes]
rs7292355	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8138404	1.00[EUR][1000 genomes]
rs8142101	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs916807	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	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
rs5997542	LGALS8	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30238600-30244800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr22:30243400-30245600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr22:30243600-30244800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr22:30243600-30245000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr22:30243600-30245000	Enhancers	Adipose Nuclei	Adipose
6	chr22:30244000-30245000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:30244200-30245800	Enhancers	Fetal Muscle Leg	muscle
8	chr22:30244400-30245000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr22:30244400-30245000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr22:30244600-30245000	Enhancers	Skeletal Muscle Male	skeletal muscle

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