Variant report

Variant	rs6938128
Chromosome Location	chr6:164284054-164284055
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1555228	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs16895451	0.98[ASN][1000 genomes]
rs16895454	0.98[ASN][1000 genomes]
rs56095211	0.97[ASN][1000 genomes]
rs67410945	0.97[ASN][1000 genomes]
rs67424524	0.97[ASN][1000 genomes]
rs67478587	0.98[ASN][1000 genomes]
rs6902564	0.97[ASN][1000 genomes]
rs6907455	0.98[ASN][1000 genomes]
rs6916946	0.98[ASN][1000 genomes]
rs7759591	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7772777	0.82[AFR][1000 genomes];0.81[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	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1798922	chr6:164257563-164298780	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6938128	LOC729603	cis	cerebellum	SCAN
rs6938128	UBE2Q2	trans	lymphoblastoid	RTeQTL
rs6938128	SPPL2A	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164275600-164287000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:164282000-164287000	Weak transcription	Right Ventricle	heart
3	chr6:164282000-164287200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:164282600-164284200	Enhancers	K562	blood
5	chr6:164283400-164287200	Weak transcription	Spleen	Spleen
6	chr6:164283800-164284200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:164284000-164284200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:164284000-164284200	Enhancers	HSMMtube	muscle
9	chr6:164284000-164285000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:164284000-164285000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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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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