Variant report

Variant	rs2115302
Chromosome Location	chr5:118167651-118167652
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118166469..118169075-chr5:118169340..118171077,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10447237	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10447238	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10447266	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241476	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959589	1.00[JPT][hapmap]
rs12109252	1.00[JPT][hapmap]
rs12187606	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[LWK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs12659444	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13166967	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448479	1.00[JPT][hapmap]
rs1567521	0.82[AMR][1000 genomes]
rs17132673	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17144552	1.00[JPT][hapmap]
rs17144708	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17144714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17144715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17144716	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.92[LWK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17144806	1.00[CHB][hapmap]
rs17144872	1.00[JPT][hapmap]
rs17144877	1.00[JPT][hapmap]
rs17381247	1.00[JPT][hapmap]
rs17440213	1.00[JPT][hapmap]
rs1864109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029036	1.00[JPT][hapmap]
rs2081957	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084460	1.00[JPT][hapmap]
rs2099092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370827	0.82[AMR][1000 genomes]
rs3813297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383585	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386288	1.00[ASN][1000 genomes]
rs406335	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392657	1.00[JPT][hapmap]
rs447317	0.82[AMR][1000 genomes]
rs4895183	1.00[CHB][hapmap]
rs4895184	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4895347	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4895353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895354	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55821851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55876313	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56004980	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs581887	1.00[ASN][1000 genomes]
rs6861907	0.83[AMR][1000 genomes]
rs6862297	1.00[JPT][hapmap]
rs6871241	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs6874109	1.00[CHB][hapmap]
rs6881583	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886240	0.83[AMR][1000 genomes]
rs73234489	0.83[AMR][1000 genomes]
rs73234502	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73236920	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706037	1.00[JPT][hapmap]
rs7709381	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7710339	1.00[JPT][hapmap]
rs7722027	0.81[AMR][1000 genomes]
rs7724403	1.00[JPT][hapmap]
rs7724753	1.00[JPT][hapmap]
rs822743	0.96[EUR][1000 genomes]
rs849728	1.00[ASN][1000 genomes]

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	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv599562	chr5:118122504-118230640	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2115302	DTWD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118143400-118178200	Weak transcription	Left Ventricle	heart
2	chr5:118158200-118176400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:118158400-118169200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:118160200-118171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:118160200-118178200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:118160200-118180200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:118161600-118174600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:118161600-118175600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:118167000-118167800	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links