Variant report

Variant	rs941862
Chromosome Location	chr6:70820921-70820922
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2093375	0.80[JPT][hapmap]
rs2093376	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2145904	0.86[JPT][hapmap]
rs2181011	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2208609	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3793055	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806028	0.88[MEX][hapmap]
rs3806031	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3806032	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3806033	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3806034	0.85[JPT][hapmap];0.88[MEX][hapmap]
rs3806037	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3828772	0.86[JPT][hapmap]
rs6455355	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6908849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6940436	0.86[JPT][hapmap]
rs7751501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1026836	chr6:70727747-70849014	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv830683	chr6:70743422-70941190	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs941862	L2HGDH	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70815200-70821200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:70818600-70827000	Weak transcription	Fetal Lung	lung
3	chr6:70819600-70821000	Enhancers	HSMM	muscle
4	chr6:70819800-70821000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:70819800-70821000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:70819800-70821000	Enhancers	NHDF-Ad	bronchial
7	chr6:70820000-70821000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:70820000-70822600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:70820600-70822800	Weak transcription	HSMMtube	muscle
10	chr6:70820800-70821800	Weak transcription	Fetal Muscle Leg	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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