Variant report

Variant	rs12215108
Chromosome Location	chr6:38722958-38722959
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38722850..38724981-chr6:38761101..38763461,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11751371	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11756771	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11758334	1.00[CHB][hapmap]
rs12192604	1.00[ASN][1000 genomes]
rs12192779	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12192848	1.00[ASN][1000 genomes]
rs12193813	1.00[ASN][1000 genomes]
rs12194119	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12197353	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12197467	1.00[ASN][1000 genomes]
rs12206059	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12209734	1.00[ASN][1000 genomes]
rs1738248	1.00[CHB][hapmap]
rs17552381	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17552881	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17623162	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17632688	1.00[CHB][hapmap]
rs1929899	1.00[CHD][hapmap];1.00[LWK][hapmap]
rs2092550	1.00[ASN][1000 genomes]
rs4279429	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45578845	1.00[ASN][1000 genomes]
rs55902132	1.00[ASN][1000 genomes]
rs55933840	1.00[ASN][1000 genomes]
rs56093987	1.00[ASN][1000 genomes]
rs56148146	1.00[ASN][1000 genomes]
rs56246807	1.00[ASN][1000 genomes]
rs56266437	1.00[ASN][1000 genomes]
rs56284095	1.00[ASN][1000 genomes]
rs56323406	1.00[ASN][1000 genomes]
rs579786	1.00[CHB][hapmap]
rs62396392	1.00[ASN][1000 genomes]
rs62396394	1.00[ASN][1000 genomes]
rs62396399	1.00[ASN][1000 genomes]
rs62396403	1.00[ASN][1000 genomes]
rs62396404	1.00[ASN][1000 genomes]
rs62396406	1.00[ASN][1000 genomes]
rs62396408	1.00[ASN][1000 genomes]
rs6933930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs72856585	1.00[ASN][1000 genomes]
rs72856596	1.00[ASN][1000 genomes]
rs72856597	1.00[ASN][1000 genomes]
rs72856598	1.00[ASN][1000 genomes]
rs72858234	1.00[ASN][1000 genomes]
rs72858240	1.00[ASN][1000 genomes]
rs72858280	1.00[ASN][1000 genomes]
rs72858282	1.00[ASN][1000 genomes]
rs72858286	1.00[ASN][1000 genomes]
rs72858288	1.00[ASN][1000 genomes]
rs72858292	1.00[ASN][1000 genomes]
rs72858299	1.00[ASN][1000 genomes]
rs7773144	1.00[ASN][1000 genomes]
rs991766	1.00[CHB][hapmap];1.00[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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12215108	TFEB	cis	cerebellum	SCAN
rs12215108	MDGA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38706200-38738600	Weak transcription	K562	blood
2	chr6:38722400-38724200	Enhancers	HMEC	breast
3	chr6:38722400-38724200	Enhancers	NHEK	skin
4	chr6:38722600-38723400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38722600-38724200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:38722600-38724200	Enhancers	Stomach Mucosa	stomach
7	chr6:38722800-38723800	Enhancers	Fetal Kidney	kidney

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