Variant report

Variant	rs12294339
Chromosome Location	chr11:34860199-34860200
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	chr11:34846388..34848890-chr11:34858178..34860592,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10488805	1.00[ASN][1000 genomes]
rs1049333	0.90[ASN][1000 genomes]
rs10836316	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836317	0.81[EUR][1000 genomes]
rs11032891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032894	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032895	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032898	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032899	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032903	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032907	0.83[ASN][1000 genomes]
rs11032939	1.00[ASN][1000 genomes]
rs11032956	1.00[ASN][1000 genomes]
rs11032958	1.00[ASN][1000 genomes]
rs11032959	1.00[ASN][1000 genomes]
rs11032960	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11032961	1.00[ASN][1000 genomes]
rs11032963	1.00[ASN][1000 genomes]
rs11032970	1.00[ASN][1000 genomes]
rs11602364	0.87[EUR][1000 genomes]
rs11607986	0.81[EUR][1000 genomes]
rs12271867	1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12272820	1.00[ASN][1000 genomes]
rs12273167	1.00[ASN][1000 genomes]
rs12274680	1.00[ASN][1000 genomes]
rs12276679	1.00[ASN][1000 genomes]
rs12278318	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12279952	1.00[ASN][1000 genomes]
rs12280958	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12284844	1.00[ASN][1000 genomes]
rs12290759	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12291039	1.00[ASN][1000 genomes]
rs12292931	1.00[ASN][1000 genomes]
rs12292993	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12294397	1.00[ASN][1000 genomes]
rs1509659	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509660	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509661	0.83[EUR][1000 genomes]
rs16926365	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16926479	1.00[ASN][1000 genomes]
rs16926673	0.90[ASN][1000 genomes]
rs17362114	1.00[ASN][1000 genomes]
rs17364197	0.90[ASN][1000 genomes]
rs17436343	0.90[ASN][1000 genomes]
rs17711539	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17712273	1.00[ASN][1000 genomes]
rs17783998	0.87[EUR][1000 genomes]
rs17784324	0.82[EUR][1000 genomes]
rs1828299	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077926	0.83[ASN][1000 genomes]
rs41512444	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4534556	0.83[EUR][1000 genomes]
rs55796371	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55911702	0.83[EUR][1000 genomes]
rs56061305	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56922113	1.00[ASN][1000 genomes]
rs57611620	1.00[ASN][1000 genomes]
rs58127349	1.00[ASN][1000 genomes]
rs59676516	1.00[ASN][1000 genomes]
rs61760973	1.00[ASN][1000 genomes]
rs61882175	1.00[ASN][1000 genomes]
rs6484738	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106831	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111695	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114359	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7114970	0.91[ASN][1000 genomes]
rs7115217	1.00[ASN][1000 genomes]
rs7115749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119807	1.00[ASN][1000 genomes]
rs7120509	1.00[ASN][1000 genomes]
rs7122048	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123029	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124099	1.00[ASN][1000 genomes]
rs7124428	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7129517	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129533	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130678	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130774	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131229	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131272	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72922479	0.87[EUR][1000 genomes]
rs72922482	0.87[EUR][1000 genomes]
rs72924508	0.82[EUR][1000 genomes]
rs7924969	1.00[ASN][1000 genomes]
rs7927857	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7929287	1.00[ASN][1000 genomes]
rs7932461	1.00[ASN][1000 genomes]
rs7936426	1.00[ASN][1000 genomes]
rs7936983	1.00[ASN][1000 genomes]
rs7941937	1.00[ASN][1000 genomes]
rs7945524	1.00[ASN][1000 genomes]
rs7947848	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12294339	APIP	cis	Thyroid	GTEx
rs12294339	APIP	cis	Nerve Tibial	GTEx
rs12294339	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs12294339	APIP	cis	Heart Left Ventricle	GTEx
rs12294339	APIP	cis	Artery Tibial	GTEx
rs12294339	APIP	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34858000-34861200	Enhancers	Esophagus	oesophagus
2	chr11:34858200-34860800	Enhancers	HepG2	liver
3	chr11:34859000-34909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:34859200-34863400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:34859400-34862200	Weak transcription	Pancreas	Pancrea
6	chr11:34859400-34871800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:34859800-34863600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links