Variant report

Variant	rs1146609
Chromosome Location	chr1:76241053-76241054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11161598	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146598	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146607	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146610	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146617	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146630	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1146631	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1146632	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146634	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146636	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146637	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146643	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1146644	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12092388	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463812	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552289	0.90[EUR][1000 genomes];1.00[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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv2763563	chr1:76229839-76245374	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1146609	MSH4	cis	Artery Tibial	GTEx
rs1146609	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs1146609	MSH4	cis	Muscle Skeletal	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76227400-76249800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:76232800-76243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:76234600-76241200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:76238000-76241200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:76238200-76241400	Weak transcription	NHEK	skin
6	chr1:76240600-76241400	Enhancers	K562	blood
7	chr1:76241000-76241400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:76241000-76241800	Enhancers	Muscle Satellite Cultured Cells	--

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

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