Variant report

Variant	rs7936185
Chromosome Location	chr11:64305452-64305453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11231808	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11231814	1.00[CHB][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231815	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11231816	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362644	0.92[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12363578	0.92[ASN][1000 genomes]
rs12417589	0.96[EUR][1000 genomes]
rs12789978	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17372915	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2078267	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs2164495	1.00[ASN][1000 genomes]
rs34484509	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34812986	1.00[ASN][1000 genomes]
rs4930194	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4930195	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4930420	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930423	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930426	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6591859	0.92[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7102027	0.85[ASN][1000 genomes]
rs7123852	0.96[EUR][1000 genomes]
rs7124676	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs71456318	1.00[ASN][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	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1035485	chr11:64228847-64354869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv897692	chr11:64305452-64386526	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7936185	RTN3	cis	parietal	SCAN
rs7936185	SNORD25	cis	cerebellum	SCAN
rs7936185	MARK2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64299800-64305600	Weak transcription	Fetal Thymus	thymus
2	chr11:64302400-64306000	Weak transcription	Placenta	Placenta
3	chr11:64302600-64306800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:64302800-64306000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:64303800-64305800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:64304000-64305600	Enhancers	Hela-S3	cervix
7	chr11:64304000-64305800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:64304000-64308400	Enhancers	Primary hematopoietic stem cells	blood
9	chr11:64304000-64310800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr11:64304400-64306000	Weak transcription	Aorta	Aorta
11	chr11:64305000-64311200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:64305200-64307200	Enhancers	Brain Hippocampus Middle	brain
13	chr11:64305200-64307600	Enhancers	Adipose Nuclei	Adipose
14	chr11:64305400-64305800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr11:64305400-64306200	Enhancers	Brain Substantia Nigra	brain
16	chr11:64305400-64306400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr11:64305400-64306800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:64305400-64307000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:64305400-64307800	Enhancers	Fetal Brain Female	brain
20	chr11:64305400-64308000	Enhancers	Fetal Brain Male	brain

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