Variant report

Variant	rs10934568
Chromosome Location	chr3:121696035-121696036
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	chr3:121638677..121641457-chr3:121694766..121696905,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263678	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10049074	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10934562	0.83[AMR][1000 genomes]
rs10934570	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1143670	0.81[AMR][1000 genomes]
rs1143671	0.81[AMR][1000 genomes]
rs1143672	0.81[AMR][1000 genomes]
rs11718322	0.87[AMR][1000 genomes]
rs11914993	0.81[AMR][1000 genomes]
rs11920521	0.81[AMR][1000 genomes]
rs11920547	0.81[AMR][1000 genomes]
rs12490565	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12637573	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074085	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1316301	0.81[AMR][1000 genomes]
rs1316397	0.81[AMR][1000 genomes]
rs1357531	0.81[AMR][1000 genomes]
rs1881999	0.81[AMR][1000 genomes]
rs1882002	0.81[AMR][1000 genomes]
rs1882003	0.81[AMR][1000 genomes]
rs1882004	0.81[AMR][1000 genomes]
rs1920289	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920302	0.81[AMR][1000 genomes]
rs1920317	0.81[AMR][1000 genomes]
rs1920318	0.81[AMR][1000 genomes]
rs1920319	0.81[AMR][1000 genomes]
rs2049330	0.81[AMR][1000 genomes]
rs2049331	0.81[AMR][1000 genomes]
rs2141614	0.81[JPT][hapmap]
rs2257109	0.81[AMR][1000 genomes]
rs2257115	0.81[AMR][1000 genomes]
rs2257119	0.81[AMR][1000 genomes]
rs2257120	0.81[AMR][1000 genomes]
rs2257123	0.81[AMR][1000 genomes]
rs2257124	0.81[AMR][1000 genomes]
rs2257132	0.81[AMR][1000 genomes]
rs2257212	0.81[AMR][1000 genomes]
rs2257214	0.81[AMR][1000 genomes]
rs2262494	0.81[AMR][1000 genomes]
rs2293612	0.81[AMR][1000 genomes]
rs2293614	0.81[AMR][1000 genomes]
rs2293615	0.81[AMR][1000 genomes]
rs2293616	0.81[AMR][1000 genomes]
rs2332034	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2332036	0.82[AMR][1000 genomes]
rs2332044	0.81[AMR][1000 genomes]
rs2332046	0.81[AMR][1000 genomes]
rs2332049	0.81[AMR][1000 genomes]
rs2332050	0.81[AMR][1000 genomes]
rs2332051	0.81[AMR][1000 genomes]
rs2332052	0.81[AMR][1000 genomes]
rs2332056	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs2689272	0.81[AMR][1000 genomes]
rs2689273	0.81[AMR][1000 genomes]
rs2689281	0.81[AMR][1000 genomes]
rs2689282	0.81[AMR][1000 genomes]
rs2689283	0.81[AMR][1000 genomes]
rs2689284	0.81[AMR][1000 genomes]
rs2689287	0.81[AMR][1000 genomes]
rs2689288	0.81[AMR][1000 genomes]
rs2689289	0.81[AMR][1000 genomes]
rs2689291	0.81[AMR][1000 genomes]
rs2689292	0.81[AMR][1000 genomes]
rs2700416	0.81[AMR][1000 genomes]
rs2700420	0.81[AMR][1000 genomes]
rs2700421	0.81[AMR][1000 genomes]
rs2700424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2700425	0.81[AMR][1000 genomes]
rs2700426	0.81[AMR][1000 genomes]
rs2877566	0.81[AMR][1000 genomes]
rs2877568	0.81[AMR][1000 genomes]
rs3762819	0.81[AMR][1000 genomes]
rs3762821	0.85[AMR][1000 genomes]
rs3762822	0.81[AMR][1000 genomes]
rs3792596	0.81[AMR][1000 genomes]
rs3792597	0.85[AMR][1000 genomes]
rs3817599	0.90[JPT][hapmap]
rs3817601	0.81[AMR][1000 genomes]
rs3932367	0.81[AMR][1000 genomes]
rs4325959	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59823080	0.85[AMR][1000 genomes]
rs6438687	0.81[AMR][1000 genomes]
rs6765799	0.81[AMR][1000 genomes]
rs6770719	0.81[JPT][hapmap]
rs6793566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803757	0.81[AMR][1000 genomes]
rs7637569	0.81[AMR][1000 genomes]
rs7646346	0.82[CHB][hapmap]
rs866926	0.81[AMR][1000 genomes]
rs866927	0.81[AMR][1000 genomes]
rs866929	0.81[AMR][1000 genomes]
rs874741	0.82[AMR][1000 genomes]
rs874742	0.82[AMR][1000 genomes]
rs9289182	0.83[AMR][1000 genomes]
rs9289183	0.81[AMR][1000 genomes]
rs9811389	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9811473	0.81[AMR][1000 genomes]
rs9812515	0.81[AMR][1000 genomes]
rs9812694	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9812869	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816071	0.81[AMR][1000 genomes]
rs9822474	0.83[AMR][1000 genomes]
rs9824120	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9825193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9828753	0.81[AMR][1000 genomes]
rs9829070	0.81[AMR][1000 genomes]
rs9836339	0.81[AMR][1000 genomes]
rs9844039	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9845790	0.83[AMR][1000 genomes]
rs9850685	0.82[AMR][1000 genomes]
rs9856253	0.81[AMR][1000 genomes]
rs9862977	0.81[AMR][1000 genomes]
rs9863154	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9863155	0.81[AMR][1000 genomes]
rs9866936	0.81[AMR][1000 genomes]
rs9867460	0.85[AMR][1000 genomes]
rs9870245	0.83[AMR][1000 genomes]
rs9871534	0.81[AMR][1000 genomes]
rs9871743	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10934568	SLC15A2	cis	Artery Tibial	GTEx
rs10934568	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs10934568	SLC15A2	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121686000-121698200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:121694000-121697200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:121694200-121697200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:121695200-121697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:121695200-121697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:121695200-121698000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:121695200-121698600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:121695400-121698000	Weak transcription	NHEK	skin
9	chr3:121695400-121698400	Weak transcription	Pancreas	Pancrea
10	chr3:121695600-121698000	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links