Variant report

Variant	rs1828298
Chromosome Location	chr11:34870439-34870440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34831080..34832844-chr11:34868501..34870661,2	K562	blood:
2	chr11:34863977..34866462-chr11:34870377..34873238,2	MCF-7	breast:
3	chr11:34868671..34870522-chr11:34876282..34878999,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1396880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509662	0.82[ASN][1000 genomes]
rs1549789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549791	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1553757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553758	0.89[ASN][1000 genomes]
rs1553759	0.82[ASN][1000 genomes]
rs1553760	0.82[ASN][1000 genomes]
rs1553761	0.80[ASN][1000 genomes]
rs1553762	0.82[ASN][1000 genomes]
rs1858166	0.89[ASN][1000 genomes]
rs2033355	0.82[ASN][1000 genomes]
rs2116085	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2163374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163375	0.80[ASN][1000 genomes]
rs2421743	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915177	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915178	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915179	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915180	0.89[ASN][1000 genomes]
rs2915237	0.80[ASN][1000 genomes]
rs2915238	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941040	0.92[ASN][1000 genomes]
rs2941041	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941042	0.89[ASN][1000 genomes]
rs2941043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941044	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941045	0.85[ASN][1000 genomes]
rs2941054	0.86[ASN][1000 genomes]
rs2941055	0.85[ASN][1000 genomes]
rs2941056	0.89[ASN][1000 genomes]
rs2941057	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941058	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941059	0.82[ASN][1000 genomes]
rs2941060	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941061	0.86[ASN][1000 genomes]
rs2956074	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2956076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956078	0.90[ASN][1000 genomes]
rs2956079	0.80[ASN][1000 genomes]
rs2956080	0.86[ASN][1000 genomes]
rs2956086	0.86[ASN][1000 genomes]
rs7932442	0.85[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1828298	APIP	cis	Heart Left Ventricle	GTEx
rs1828298	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs1828298	APIP	cis	Esophagus Muscularis	GTEx
rs1828298	PDHX	Cis_1M	lymphoblastoid	RTeQTL
rs1828298	APIP	cis	Nerve Tibial	GTEx
rs1828298	APIP	cis	lung	GTEx
rs1828298	LOC728766///PRDM15	trans	lymphoblastoid	RTeQTL
rs1828298	APIP	cis	Thyroid	GTEx
rs1828298	APIP	cis	Artery Tibial	GTEx
rs1828298	APIP	cis	Artery Aorta	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34859000-34909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:34859400-34871800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:34869800-34871600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links