Variant report

Variant	rs60625846
Chromosome Location	chr3:161084525-161084526
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161040142..161042354-chr3:161082440..161084651,2	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160970393..160971997-chr3:161083737..161085470,2	MCF-7	breast:
4	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
5	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10513564	0.85[EUR][1000 genomes]
rs10936227	0.84[EUR][1000 genomes]
rs11710489	0.88[EUR][1000 genomes]
rs11711413	0.82[EUR][1000 genomes]
rs11711695	0.85[EUR][1000 genomes]
rs11715591	0.86[EUR][1000 genomes]
rs11718905	0.85[EUR][1000 genomes]
rs11929238	0.85[EUR][1000 genomes]
rs13059340	0.86[EUR][1000 genomes]
rs13059386	0.81[EUR][1000 genomes]
rs13062740	0.84[EUR][1000 genomes]
rs13073147	0.85[EUR][1000 genomes]
rs13076251	0.88[EUR][1000 genomes]
rs13084731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382429	0.81[EUR][1000 genomes]
rs1450519	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1450521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1450522	0.88[EUR][1000 genomes]
rs1450523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478566	0.84[EUR][1000 genomes]
rs16832082	0.85[EUR][1000 genomes]
rs2054710	0.88[EUR][1000 genomes]
rs2100238	0.85[EUR][1000 genomes]
rs2122527	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404341	0.88[EUR][1000 genomes]
rs2404342	0.88[EUR][1000 genomes]
rs34016896	0.82[EUR][1000 genomes]
rs34771618	0.85[EUR][1000 genomes]
rs34896809	0.85[EUR][1000 genomes]
rs34972965	0.81[EUR][1000 genomes]
rs35100811	0.88[EUR][1000 genomes]
rs4856701	0.84[EUR][1000 genomes]
rs4856703	0.85[EUR][1000 genomes]
rs4856756	0.82[EUR][1000 genomes]
rs4856757	0.82[EUR][1000 genomes]
rs4856769	0.82[EUR][1000 genomes]
rs67460515	0.88[EUR][1000 genomes]
rs6780536	0.85[EUR][1000 genomes]
rs7610800	0.82[EUR][1000 genomes]
rs7610985	0.86[EUR][1000 genomes]
rs7630356	0.82[EUR][1000 genomes]
rs7647118	0.81[EUR][1000 genomes]
rs7647374	0.81[EUR][1000 genomes]
rs7648279	0.81[EUR][1000 genomes]
rs9844862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv963570	chr3:161076656-161088849	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60625846	SPTSSB	cis	Heart Left Ventricle	GTEx
rs60625846	SPTSSB	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161081800-161087200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:161083000-161084800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr3:161083200-161084600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:161083200-161084800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:161084000-161085200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:161084000-161085400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:161084200-161084600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:161084400-161085600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:161084400-161087400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:161084400-161088400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:161084400-161088800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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