Variant report

Variant	rs1403104
Chromosome Location	chr3:156986803-156986804
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	chr3:156876934..156879709-chr3:156982846..156986882,3	K562	blood:

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10451916	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs1046938	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs10513507	0.88[CEU][hapmap]
rs10513508	0.82[MEX][hapmap]
rs1060543	0.87[CEU][hapmap]
rs10804777	0.91[CHB][hapmap]
rs10936063	0.87[CEU][hapmap]
rs10936066	0.87[CEU][hapmap]
rs1157738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12488480	0.86[CEU][hapmap]
rs12492801	0.87[CEU][hapmap]
rs12493531	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496111	0.85[CEU][hapmap]
rs12629589	0.81[AMR][1000 genomes]
rs12632562	0.82[CEU][hapmap]
rs12633429	0.87[CEU][hapmap]
rs12637932	0.91[CHB][hapmap]
rs13061214	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs13081036	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs13081038	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs1392799	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs1403103	0.80[EUR][1000 genomes]
rs1403106	0.87[CEU][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs1403108	0.82[MEX][hapmap]
rs1522392	0.82[MEX][hapmap]
rs1568611	0.80[AMR][1000 genomes]
rs1587535	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1608127	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs16827308	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs16827322	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1995304	0.87[CEU][hapmap]
rs2047647	0.87[CHB][hapmap]
rs2874616	0.87[CEU][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs3749214	0.88[CEU][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs3935750	0.87[CEU][hapmap]
rs4256081	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679788	0.83[CEU][hapmap]
rs4680340	0.87[CEU][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap]
rs4680342	0.81[CEU][hapmap]
rs4680343	0.87[CEU][hapmap]
rs4680345	0.86[CEU][hapmap]
rs4680346	0.87[CEU][hapmap]
rs4680347	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680349	0.81[AMR][1000 genomes]
rs4680352	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs5003893	0.87[CEU][hapmap]
rs56143236	0.80[AMR][1000 genomes]
rs58666615	0.84[EUR][1000 genomes]
rs62276493	0.88[EUR][1000 genomes]
rs62276528	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279635	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6441115	0.87[CEU][hapmap]
rs6441116	0.87[CEU][hapmap]
rs6441123	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs6767619	0.91[CEU][hapmap]
rs6768074	0.87[CEU][hapmap]
rs6781682	0.83[CEU][hapmap]
rs6788214	0.84[CEU][hapmap]
rs6795007	0.80[LWK][hapmap]
rs6799567	0.82[MEX][hapmap]
rs6805114	0.82[CEU][hapmap]
rs6805989	0.87[CEU][hapmap]
rs6808457	0.87[CEU][hapmap]
rs6809003	0.81[CEU][hapmap];0.95[TSI][hapmap]
rs6809307	0.87[CEU][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap]
rs6809394	0.80[CEU][hapmap];0.93[TSI][hapmap]
rs68122740	0.88[EUR][1000 genomes]
rs73154652	0.87[EUR][1000 genomes]
rs73154671	0.82[AMR][1000 genomes]
rs73154682	0.85[AMR][1000 genomes]
rs7610214	0.83[AMR][1000 genomes]
rs7619892	0.81[AMR][1000 genomes]
rs7621912	0.87[CEU][hapmap]
rs7625059	0.88[CEU][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs7638194	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs7647643	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs7648599	0.87[CEU][hapmap]
rs7649737	0.80[AMR][1000 genomes]
rs7652298	0.87[CEU][hapmap];0.85[AMR][1000 genomes]
rs872652	0.91[CHB][hapmap]
rs8925	0.87[CEU][hapmap]
rs924516	0.81[AMR][1000 genomes]
rs924517	0.80[TSI][hapmap]
rs949854	0.83[AMR][1000 genomes]
rs9827676	0.81[CEU][hapmap]
rs9867618	0.80[TSI][hapmap]

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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1403104	PTX3	cis	parietal	SCAN
rs1403104	SMC4	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156967200-156989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:156967200-157000000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:156967200-157000000	Weak transcription	NH-A	brain
4	chr3:156967200-157007800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:156979600-156997000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:156981200-156991400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:156981600-156991000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:156982400-156992800	Weak transcription	Osteobl	bone
9	chr3:156982400-156997000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:156984200-156998200	Weak transcription	HUVEC	blood vessel
11	chr3:156986000-156987600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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