Variant report

Variant	rs7046597
Chromosome Location	chr9:93206737-93206738
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10821409	0.81[EUR][1000 genomes]
rs10821452	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426507	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1529333	0.81[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1930923	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2217094	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2217095	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2386532	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7029610	0.84[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7030038	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7047032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724248	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv614853	chr9:93183404-93266508	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7046597	RP11-389K14.3	cis	lung	GTEx
rs7046597	GOLM1	cis	cerebellum	SCAN
rs7046597	SPTLC1	cis	parietal	SCAN
rs7046597	IARS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93196200-93220800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:93204600-93210200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:93205600-93207200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:93205800-93207000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:93205800-93207800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:93206000-93211400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:93206400-93222600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:93206600-93207800	Enhancers	H1 BMP4 Derived Mesendoderm 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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