Variant report

Variant	rs3925003
Chromosome Location	chr6:55422618-55422619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10755781	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10807496	0.85[AFR][1000 genomes]
rs10948936	0.81[CHB][hapmap]
rs10948941	0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10948942	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12193162	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12195913	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12202288	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13206666	0.81[CHB][hapmap]
rs3800027	0.81[CHB][hapmap]
rs4075708	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4075709	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4144579	0.93[AFR][1000 genomes]
rs4144580	0.87[AFR][1000 genomes]
rs4283891	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4314500	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4342412	0.85[AFR][1000 genomes]
rs4346853	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4360137	0.88[ASN][1000 genomes]
rs4382261	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4388287	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4398737	0.87[AFR][1000 genomes]
rs4410726	0.86[AFR][1000 genomes]
rs4431436	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4445058	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4454140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479933	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4489148	0.85[AFR][1000 genomes]
rs4489157	0.82[ASN][1000 genomes]
rs4501434	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4521577	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4537142	0.81[CHB][hapmap]
rs4543375	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4569966	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588676	0.97[ASN][1000 genomes]
rs4596474	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4599642	0.85[AFR][1000 genomes]
rs6459083	0.83[AFR][1000 genomes]
rs6459084	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6905376	0.82[ASN][1000 genomes]
rs6914816	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6919350	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7741830	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7755709	0.87[AFR][1000 genomes]
rs7776071	0.87[AFR][1000 genomes]
rs9296793	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9367640	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9367641	0.93[AFR][1000 genomes]
rs9367642	0.87[AFR][1000 genomes]
rs9370438	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9382506	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9396108	0.87[AFR][1000 genomes]
rs9464265	0.85[AFR][1000 genomes]
rs9475342	0.88[ASN][1000 genomes]
rs9475344	0.88[ASN][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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv948358	chr6:55351282-55477277	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1026411	chr6:55372845-55653498	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3925003	GCLC	cis	parietal	SCAN
rs3925003	GCM1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55419600-55433600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:55421200-55423000	Enhancers	Fetal Heart	heart
3	chr6:55422400-55423400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:55422600-55423000	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr6:55422600-55433400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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