Variant report

Variant	rs358898
Chromosome Location	chr3:155400884-155400885
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	chr3:155398889..155402397-chr3:155403887..155406170,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1005736	0.81[ASN][1000 genomes]
rs1007920	0.80[ASN][1000 genomes]
rs12486000	0.82[AMR][1000 genomes]
rs12488043	0.80[ASN][1000 genomes]
rs12488087	0.80[ASN][1000 genomes]
rs12490748	0.81[ASN][1000 genomes]
rs13076587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13084995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13087389	0.85[ASN][1000 genomes]
rs13089059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13095140	0.80[ASN][1000 genomes]
rs1519532	0.81[ASN][1000 genomes]
rs1519533	0.81[ASN][1000 genomes]
rs1519534	0.81[ASN][1000 genomes]
rs1519535	0.81[ASN][1000 genomes]
rs1568360	0.80[ASN][1000 genomes]
rs1879090	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879091	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879092	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2203886	0.85[ASN][1000 genomes]
rs2222275	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34810038	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs358704	0.83[ASN][1000 genomes]
rs358706	0.86[ASN][1000 genomes]
rs358707	0.86[ASN][1000 genomes]
rs358708	0.86[ASN][1000 genomes]
rs358727	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs358728	0.81[AMR][1000 genomes]
rs358896	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358897	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358899	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358902	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358904	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs358905	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358906	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358910	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358911	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407212	0.84[ASN][1000 genomes]
rs4083041	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412664	0.86[ASN][1000 genomes]
rs417877	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426069	0.87[ASN][1000 genomes]
rs60592119	0.81[ASN][1000 genomes]
rs6441006	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67428377	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772682	0.80[ASN][1000 genomes]
rs6777741	0.83[ASN][1000 genomes]
rs67955071	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808257	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7428196	0.87[ASN][1000 genomes]
rs7645831	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155395000-155416800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:155395200-155412000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:155399400-155401000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:155399400-155401000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:155399600-155401000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:155400600-155404000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:155400600-155408800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:155400800-155401200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:155400800-155401400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:155400800-155402200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr3:155400800-155418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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