Variant report

Variant	rs6441318
Chromosome Location	chr3:100253871-100253872
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	chr3:100241152..100243622-chr3:100252905..100255777,2	MCF-7	breast:
2	chr3:100053176..100055387-chr3:100252864..100255166,2	K562	blood:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11706258	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710281	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713258	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715555	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719592	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11923487	0.82[ASN][1000 genomes]
rs12634314	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12634317	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12635025	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12635026	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12636452	0.96[ASN][1000 genomes]
rs13093980	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28722928	0.81[ASN][1000 genomes]
rs4077302	0.81[ASN][1000 genomes]
rs4129205	0.82[ASN][1000 genomes]
rs4928048	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928049	0.81[ASN][1000 genomes]
rs4928063	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928064	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928065	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928110	0.96[ASN][1000 genomes]
rs4928111	0.96[ASN][1000 genomes]
rs4928112	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55764247	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55789829	0.96[ASN][1000 genomes]
rs56736439	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57075146	0.81[ASN][1000 genomes]
rs57404153	0.82[ASN][1000 genomes]
rs57671998	0.81[ASN][1000 genomes]
rs58689996	0.96[ASN][1000 genomes]
rs58789183	0.95[ASN][1000 genomes]
rs59281247	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60375749	0.81[ASN][1000 genomes]
rs60511852	0.96[ASN][1000 genomes]
rs61403861	0.81[ASN][1000 genomes]
rs62274560	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274561	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274575	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62278361	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441321	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441328	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441329	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66747627	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66828943	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67348505	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6763638	0.82[ASN][1000 genomes]
rs6796541	0.81[ASN][1000 genomes]
rs6799879	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6799882	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6799992	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6802787	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6803109	0.81[ASN][1000 genomes]
rs6805186	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6807804	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808426	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72929220	0.81[ASN][1000 genomes]
rs7426462	0.82[ASN][1000 genomes]
rs7427360	0.82[ASN][1000 genomes]
rs7429277	0.89[ASN][1000 genomes]
rs7429915	0.81[ASN][1000 genomes]
rs7431846	0.93[ASN][1000 genomes]
rs7432710	0.82[ASN][1000 genomes]
rs7433589	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7433875	0.82[ASN][1000 genomes]
rs7611100	0.87[ASN][1000 genomes]
rs7617909	0.82[ASN][1000 genomes]
rs7618030	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7622658	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7625717	0.81[ASN][1000 genomes]
rs7631877	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644235	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645690	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645700	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647492	0.82[ASN][1000 genomes]
rs7647499	0.86[ASN][1000 genomes]
rs7650265	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653126	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814643	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819246	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820745	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9823159	0.81[ASN][1000 genomes]
rs9825818	0.82[ASN][1000 genomes]
rs9843498	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9845649	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855549	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865411	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9865776	0.81[ASN][1000 genomes]
rs9870803	0.81[ASN][1000 genomes]
rs9880036	0.81[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	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6441318	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs6441318	NAP5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle
2	chr3:100241000-100299800	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:100242400-100265000	Weak transcription	HepG2	liver
4	chr3:100242400-100268000	Weak transcription	Ovary	ovary
5	chr3:100244600-100261400	Weak transcription	Fetal Lung	lung
6	chr3:100244800-100255400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:100244800-100257800	Weak transcription	Spleen	Spleen
8	chr3:100244800-100267000	Weak transcription	HSMM	muscle
9	chr3:100245400-100255800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:100245600-100254600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:100250800-100255200	Enhancers	NHDF-Ad	bronchial
12	chr3:100251000-100257400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:100251400-100255000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:100251400-100255600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:100251600-100254200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:100251800-100257000	Enhancers	Hela-S3	cervix
17	chr3:100252000-100254000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:100252000-100254000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:100252000-100254200	Enhancers	NHEK	skin
20	chr3:100252600-100254000	Strong transcription	Fetal Stomach	stomach
21	chr3:100253200-100254000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:100253200-100255200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:100253200-100256200	Enhancers	Liver	Liver
24	chr3:100253200-100257400	Enhancers	HMEC	breast
25	chr3:100253400-100254800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:100253600-100254200	Enhancers	Osteobl	bone
27	chr3:100253600-100254400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:100253600-100255200	Enhancers	Adipose Nuclei	Adipose
29	chr3:100253800-100254200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:100253800-100254600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:100253800-100255000	Weak transcription	Pancreas	Pancrea
32	chr3:100253800-100289000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:100253800-100289000	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links