Variant report

Variant	rs12362644
Chromosome Location	chr11:64312153-64312154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64311826..64313393-chr11:64315068..64317928,2	MCF-7	breast:
2	11:64307888-64312302..11:64426650-64437729	K562	blood:
3	11:64307888-64312302..11:64523887-64530985	Hela-S3	cervix:
4	11:64307888-64312302..11:64402707-64415880	H1-hESC	embryonic stem cell:	embryo
5	11:64307888-64312302..11:64415880-64426617	H1-hESC	embryonic stem cell:	embryo
6	11:64207610-64216678..11:64307888-64312302	K562	blood:
7	11:64307888-64312302..11:64501239-64517861	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000068976	Chromatin interaction
ENSG00000110076	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000237410	Chromatin interaction
ENSG00000181908	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11231808	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11231814	0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11231815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231816	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11231822	0.97[ASN][1000 genomes]
rs12417589	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12808503	0.97[ASN][1000 genomes]
rs17300741	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17300895	0.92[ASN][1000 genomes]
rs2277312	0.97[ASN][1000 genomes]
rs3759053	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3782099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4930194	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930195	1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930420	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4930423	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57827982	0.95[ASN][1000 genomes]
rs6591859	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123852	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7929308	0.97[ASN][1000 genomes]
rs7936185	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7940321	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7943154	1.00[CHB][hapmap];0.92[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12362644	RTN3	cis	parietal	SCAN
rs12362644	SNORD25	cis	cerebellum	SCAN
rs12362644	CDK2AP2	cis	parietal	SCAN
rs12362644	MARK2	cis	parietal	SCAN
rs12362644	CST6	cis	cerebellum	SCAN
rs12362644	RAB3IL1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64307400-64315600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:64310400-64313000	Weak transcription	Esophagus	oesophagus
3	chr11:64310600-64313000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:64310600-64314400	Enhancers	NHEK	skin
5	chr11:64311000-64312200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:64311000-64312200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:64311200-64312200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:64311200-64312200	Weak transcription	Placenta	Placenta
9	chr11:64311800-64314400	Enhancers	HMEC	breast
10	chr11:64312000-64312600	Bivalent Enhancer	HepG2	liver
11	chr11:64312000-64312800	Enhancers	Hela-S3	cervix

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