Variant report

Variant	rs4398624
Chromosome Location	chr5:152018343-152018344
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	chr5:152014610..152016353-chr5:152016707..152018951,3	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10054152	0.82[AMR][1000 genomes]
rs10056328	0.83[AMR][1000 genomes]
rs10155517	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10515675	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515676	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11167584	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11956651	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188564	0.82[EUR][1000 genomes]
rs13359939	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13361438	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452991	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17453481	0.93[EUR][1000 genomes]
rs17453530	0.93[EUR][1000 genomes]
rs17453740	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17453775	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17454420	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17455800	0.85[EUR][1000 genomes]
rs17550343	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17565365	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17565470	0.85[EUR][1000 genomes]
rs17565505	0.83[EUR][1000 genomes]
rs17565693	0.90[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2961756	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2961760	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2961765	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2961766	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2964230	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2964231	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3923209	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4246033	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4391148	0.82[AMR][1000 genomes]
rs4406125	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478308	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4484412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4557395	0.94[EUR][1000 genomes]
rs4580766	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4610448	0.81[AMR][1000 genomes]
rs4618416	0.82[AMR][1000 genomes]
rs4958316	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958317	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958320	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958321	0.83[AMR][1000 genomes]
rs4958322	0.83[AMR][1000 genomes]
rs4958323	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958324	0.82[AMR][1000 genomes]
rs4958560	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958561	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958562	0.94[EUR][1000 genomes]
rs4958564	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958566	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958567	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4958568	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958569	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55648729	0.98[EUR][1000 genomes]
rs55786399	0.93[EUR][1000 genomes]
rs56014830	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67979431	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6863717	0.82[AMR][1000 genomes]
rs6869035	0.82[AMR][1000 genomes]
rs6869129	0.82[AMR][1000 genomes]
rs6871699	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876403	0.80[EUR][1000 genomes]
rs6876723	0.87[ASN][1000 genomes]
rs6884556	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885111	0.82[AMR][1000 genomes]
rs6885419	0.82[AMR][1000 genomes]
rs6895969	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795376	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72795379	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72795389	0.93[EUR][1000 genomes]
rs72797226	0.91[ASN][1000 genomes]
rs72797233	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797237	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797241	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797243	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797251	0.97[EUR][1000 genomes]
rs72797254	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72797262	0.98[EUR][1000 genomes]
rs72797296	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72799113	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7730088	0.82[AMR][1000 genomes]
rs9324734	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv5074	chr5:152010691-152055779	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4398624	SLC26A2	cis	cerebellum	SCAN
rs4398624	GLRA1	cis	cerebellum	SCAN
rs4398624	IL17B	cis	cerebellum	SCAN
rs4398624	IL17B	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152008400-152022800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:152011800-152021800	Weak transcription	Aorta	Aorta
3	chr5:152013600-152018400	Weak transcription	Fetal Lung	lung
4	chr5:152014600-152018400	Weak transcription	Adipose Nuclei	Adipose
5	chr5:152014800-152021000	Weak transcription	Fetal Brain Male	brain
6	chr5:152015000-152024000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:152015200-152018800	Weak transcription	Brain Germinal Matrix	brain
8	chr5:152015400-152021600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:152016800-152021200	Weak transcription	Fetal Brain Female	brain
10	chr5:152018000-152018600	Enhancers	Skeletal Muscle Female	skeletal muscle

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