Variant report

Variant	rs6945990
Chromosome Location	chr7:12159350-12159351
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10236588	0.96[EUR][1000 genomes]
rs10251182	0.83[ASN][1000 genomes]
rs10263550	0.83[ASN][1000 genomes]
rs10280578	0.83[ASN][1000 genomes]
rs10950383	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950384	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761090	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11770347	0.83[ASN][1000 genomes]
rs11771114	0.96[EUR][1000 genomes]
rs11773443	0.83[ASN][1000 genomes]
rs11977250	0.83[ASN][1000 genomes]
rs11977297	0.83[ASN][1000 genomes]
rs11980827	0.83[ASN][1000 genomes]
rs12699310	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12699311	0.83[ASN][1000 genomes]
rs13221968	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17165582	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17592324	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17650986	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1861279	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2192732	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2356053	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2356055	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356056	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35346739	0.93[ASN][1000 genomes]
rs35649285	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35828107	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36014865	0.94[EUR][1000 genomes]
rs4236267	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4236268	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4719294	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4719295	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4719296	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4721038	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4721039	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4721041	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4721042	0.91[EUR][1000 genomes]
rs6460882	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68113272	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6952511	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6956124	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7783494	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7790585	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7797675	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9638681	0.96[EUR][1000 genomes];0.82[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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv887614	chr7:11778424-12211198	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv830906	chr7:12001764-12177869	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1023608	chr7:12064114-12247520	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6945990	TMEM109	cis	Cerebellum	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12151800-12159800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:12158000-12160600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:12158000-12160600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr7:12158200-12161200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:12158800-12160600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:12159200-12159400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr7:12159200-12160400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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