Variant report

Variant	rs650567
Chromosome Location	chr3:101594402-101594403
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs14134	0.80[CHD][hapmap]
rs2926538	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929922	0.82[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617688	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs641432	0.82[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs647556	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs654102	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs662792	0.82[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs665211	0.82[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs675779	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs694936	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs771578	0.83[ASN][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs650567	SS18L2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:101583400-101598000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:101588200-101597000	Weak transcription	Liver	Liver
4	chr3:101589000-101594600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:101589000-101595800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:101590200-101600800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:101592400-101597200	Weak transcription	Stomach Mucosa	stomach
8	chr3:101592600-101595400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr3:101592600-101598000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:101592800-101595000	Weak transcription	HepG2	liver

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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