Variant report

Variant	rs1401379
Chromosome Location	chr3:156295380-156295381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156291546..156294626-chr3:156294920..156298370,3	K562	blood:
2	chr3:156291504..156293505-chr3:156294673..156297348,4	K562	blood:
3	chr3:156292781..156295460-chr3:156320968..156322481,2	K562	blood:
4	chr3:156294996..156297578-chr3:156317341..156320285,2	K562	blood:
5	chr3:156291909..156296345-chr3:156390715..156393558,5	MCF-7	breast:
6	chr3:156292876..156295853-chr3:156296167..156299089,2	MCF-7	breast:
7	chr3:156293117..156296700-chr3:156390328..156392688,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11718663	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12696038	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12696039	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13063385	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13063568	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13063746	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13092740	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13096478	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13314546	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13317303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13322475	0.88[AMR][1000 genomes]
rs1510274	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16826570	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16826572	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17367831	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1983205	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1995875	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2320894	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2320895	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34016978	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34581312	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34667319	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35907778	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62285116	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6441080	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6441081	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6650896	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6808027	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71310482	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7610493	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7615297	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7615384	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7618375	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7620297	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7633365	0.81[AMR][1000 genomes]
rs7640295	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7640363	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7652356	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs874641	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs874642	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs874662	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs874663	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9289970	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs931989	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9631440	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9812232	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9826775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831507	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9832367	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9840361	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9840524	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9840533	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9843340	0.88[AMR][1000 genomes]
rs9869703	0.86[AMR][1000 genomes]
rs9870053	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9870256	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9870575	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9882596	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877684	chr3:156294987-156344825	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1401379	TIPARP-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156293800-156296800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:156294000-156296800	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr3:156294200-156295400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:156294200-156299000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:156294400-156296800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:156294400-156300000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:156294400-156300200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:156294600-156296600	Enhancers	K562	blood
9	chr3:156294800-156296600	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:156294800-156299400	Weak transcription	GM12878-XiMat	blood
11	chr3:156295000-156296400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:156295200-156295400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:156295200-156295400	Enhancers	Primary B cells from cord blood	blood
14	chr3:156295200-156295600	Weak transcription	Stomach Mucosa	stomach
15	chr3:156295200-156295600	Enhancers	Osteobl	bone
16	chr3:156295200-156296000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:156295200-156296400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:156295200-156296600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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