Variant report

Variant	rs1251485
Chromosome Location	chr1:76503162-76503163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10782605	0.84[EUR][1000 genomes]
rs10873865	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123144	0.91[CEU][hapmap]
rs12123760	0.91[CEU][hapmap]
rs12125940	0.87[EUR][1000 genomes]
rs12126074	0.87[EUR][1000 genomes]
rs12145522	0.87[EUR][1000 genomes]
rs1251476	0.90[AFR][1000 genomes]
rs1251484	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251486	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251489	0.89[EUR][1000 genomes]
rs1251492	0.90[EUR][1000 genomes]
rs1251494	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251495	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251496	0.90[EUR][1000 genomes]
rs1251501	0.90[EUR][1000 genomes]
rs1251502	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1251504	0.90[EUR][1000 genomes]
rs1251505	0.90[EUR][1000 genomes]
rs1251506	0.89[EUR][1000 genomes]
rs1251507	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1251509	0.89[EUR][1000 genomes]
rs1251510	0.88[EUR][1000 genomes]
rs1251511	0.90[EUR][1000 genomes]
rs1251512	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251513	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251519	0.86[AFR][1000 genomes]
rs1251526	0.84[AFR][1000 genomes]
rs1251528	0.84[AFR][1000 genomes]
rs1266117	0.90[EUR][1000 genomes]
rs1340690	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1340691	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17607383	0.89[EUR][1000 genomes]
rs17659615	0.89[EUR][1000 genomes]
rs1770895	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34354538	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35318380	0.87[EUR][1000 genomes]
rs35381129	0.87[EUR][1000 genomes]
rs5022490	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60182743	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2754129	chr1:76489579-76529279	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1251485	MSH4	cis	parietal	SCAN
rs1251485	ACADM	cis	cerebellum	SCAN
rs1251485	SNORD45B	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76492600-76503400	Weak transcription	Fetal Lung	lung
2	chr1:76501600-76503400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:76501800-76503400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr1:76501800-76503600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:76501800-76504200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr1:76501800-76504400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:76502000-76503600	Enhancers	H9 Cell Line	embryonic stem cell
8	chr1:76502200-76507200	Enhancers	Fetal Intestine Large	intestine
9	chr1:76502200-76507400	Enhancers	Fetal Intestine Small	intestine
10	chr1:76502600-76503800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:76502800-76503200	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr1:76502800-76503600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:76502800-76504000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:76502800-76504200	Enhancers	Stomach Mucosa	stomach
15	chr1:76503000-76503200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:76503000-76503800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:76503000-76504200	Enhancers	Fetal Stomach	stomach
18	chr1:76503000-76504400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:76503000-76504800	Enhancers	Fetal Kidney	kidney
20	chr1:76503000-76505200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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