Variant report

Variant	rs664928
Chromosome Location	chr3:138318039-138318040
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	chr3:138313714..138315292-chr3:138315408..138318314,2	K562	blood:
2	chr3:138317841..138320703-chr3:138322061..138324398,2	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10804658	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1082034	0.84[EUR][1000 genomes]
rs1082037	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1088055	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935287	0.88[EUR][1000 genomes]
rs11717771	0.88[EUR][1000 genomes]
rs12487652	0.87[EUR][1000 genomes]
rs12487694	0.87[EUR][1000 genomes]
rs12490633	0.88[EUR][1000 genomes]
rs12497070	0.88[EUR][1000 genomes]
rs12636910	0.88[EUR][1000 genomes]
rs13101081	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1379257	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1479930	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1600511	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1672927	0.81[EUR][1000 genomes]
rs1672932	0.87[EUR][1000 genomes]
rs1672938	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1672939	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1672963	0.86[EUR][1000 genomes]
rs1673593	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1673594	0.86[EUR][1000 genomes]
rs1673607	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1673608	0.86[EUR][1000 genomes]
rs1673612	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1673622	0.88[EUR][1000 genomes]
rs1673624	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1679175	0.82[AMR][1000 genomes]
rs1720836	0.80[AMR][1000 genomes]
rs2124868	0.80[EUR][1000 genomes]
rs2348146	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2607790	0.86[EUR][1000 genomes]
rs2607795	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881793	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs361073	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361074	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361075	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361076	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361077	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4432674	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4678264	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs484698	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4894389	0.87[EUR][1000 genomes]
rs497334	0.87[EUR][1000 genomes]
rs503922	0.88[EUR][1000 genomes]
rs529615	0.88[EUR][1000 genomes]
rs537210	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs542010	0.81[EUR][1000 genomes]
rs550507	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs559313	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs564800	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs579750	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs582386	0.80[EUR][1000 genomes]
rs586946	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs587005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587331	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60513493	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs609497	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs609797	0.81[EUR][1000 genomes]
rs611134	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61699523	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs618792	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs620035	0.84[EUR][1000 genomes]
rs629884	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs634374	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs642258	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6439810	0.81[EUR][1000 genomes]
rs6771237	0.81[EUR][1000 genomes]
rs6798058	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs680070	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7625326	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7627685	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7634745	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7643973	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7653815	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs773444	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs773445	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773448	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs773449	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs773450	0.88[EUR][1000 genomes]
rs773452	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs773456	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs811322	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs811793	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs814022	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs936316	0.88[EUR][1000 genomes]
rs9681127	0.85[EUR][1000 genomes]
rs9811052	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9817419	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9827256	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9848718	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9853998	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9878436	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs664928	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs664928	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138313600-138327200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:138313800-138319000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:138313800-138327200	Weak transcription	Psoas Muscle	Psoas
4	chr3:138314000-138319000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:138314000-138319000	Weak transcription	Osteobl	bone
6	chr3:138314000-138319200	Weak transcription	Adipose Nuclei	Adipose
7	chr3:138314000-138321400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:138314000-138327000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:138314000-138327200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:138314200-138319200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:138314200-138319400	Weak transcription	Stomach Mucosa	stomach
12	chr3:138314200-138327000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:138316400-138319200	Weak transcription	Pancreas	Pancrea
14	chr3:138317200-138319000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:138318000-138321400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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