Variant report

Variant	rs1125242
Chromosome Location	chr7:47967519-47967520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11766127	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12702399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12702400	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13229586	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13239855	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13239959	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13240488	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17711336	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs17711348	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280537	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3176483	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3176493	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3176559	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3176565	0.86[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35796271	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6463456	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6945365	0.92[MEX][hapmap]
rs6956732	0.88[JPT][hapmap]
rs71547871	0.84[ASN][1000 genomes]
rs71547873	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1125242	SNORA9	cis	cerebellum	SCAN
rs1125242	UPP1	cis	cerebellum	SCAN
rs1125242	PKD1L1	cis	cerebellum	SCAN
rs1125242	NACAD	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47956400-47968600	Weak transcription	Left Ventricle	heart
3	chr7:47964000-47970800	Weak transcription	Adipose Nuclei	Adipose
4	chr7:47964800-47970600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:47965000-47972200	Weak transcription	Fetal Stomach	stomach
6	chr7:47965800-47980400	Weak transcription	Aorta	Aorta
7	chr7:47966000-47968600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:47966000-47969600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:47966200-47970800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:47966600-47974000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:47967000-47977400	Weak transcription	Right Ventricle	heart
12	chr7:47967400-47970600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links