Variant report

Variant	rs7488909
Chromosome Location	chr12:51425837-51425838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:51425824-51425881	GM20000	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51418775..51423159-chr12:51423920..51427598,6	K562	blood:
2	chr12:51425185..51426824-chr12:51428471..51430298,2	K562	blood:
3	chr12:51421539..51423905-chr12:51425266..51427769,3	MCF-7	breast:

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1005559	0.87[ASN][1000 genomes]
rs11169642	0.84[CEU][hapmap]
rs11169661	0.84[ASN][1000 genomes]
rs11169667	0.84[ASN][1000 genomes]
rs11169669	0.83[ASN][1000 genomes]
rs11169670	0.84[ASN][1000 genomes]
rs11169671	0.84[ASN][1000 genomes]
rs11169672	0.81[ASN][1000 genomes]
rs12366756	0.84[ASN][1000 genomes]
rs12371463	0.81[ASN][1000 genomes]
rs12372173	0.87[ASN][1000 genomes]
rs12827861	0.81[ASN][1000 genomes]
rs12828536	0.87[ASN][1000 genomes]
rs12830073	0.87[ASN][1000 genomes]
rs12831269	0.84[ASN][1000 genomes]
rs224565	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224577	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs224589	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs224591	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301529	0.81[ASN][1000 genomes]
rs2516742	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2630364	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319932	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35656976	0.84[ASN][1000 genomes]
rs407135	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs422637	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs422982	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs440595	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4471501	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs454520	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67133203	0.87[ASN][1000 genomes]
rs706801	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs706802	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7972406	0.81[ASN][1000 genomes]
rs7975147	0.87[ASN][1000 genomes]
rs829022	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853235	0.94[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	esv3346723	chr12:51425754-51425988	Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7488909	LETMD1	Cis_1M	lymphoblastoid	RTeQTL
rs7488909	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51422800-51432000	Weak transcription	Stomach Mucosa	stomach
2	chr12:51423800-51426400	Weak transcription	K562	blood
3	chr12:51423800-51431800	Weak transcription	Hela-S3	cervix
4	chr12:51424400-51427000	Weak transcription	HepG2	liver

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