Variant report

Variant	rs41267552
Chromosome Location	chr1:165550634-165550635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:165550112-165550646	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:165550247-165550707	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:165550127-165550754	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:165550106-165550709	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:165550247-165550746	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RXRG-1	chr1:165550592-165550738	NONHSAT007319

Variant related genes	Relation type
ENSG00000237783	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157861	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12117066	0.82[EUR][1000 genomes]
rs12119602	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12125420	0.86[AFR][1000 genomes]
rs12126717	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12131992	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12137629	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12143824	1.00[ASN][1000 genomes]
rs1326374	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1409413	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1425753	0.81[ASN][1000 genomes]
rs16846547	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16846623	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846756	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16847073	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16847083	0.98[ASN][1000 genomes]
rs16847085	0.98[ASN][1000 genomes]
rs16847110	0.98[ASN][1000 genomes]
rs16847331	0.92[AMR][1000 genomes]
rs16847398	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2152818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252342	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs285421	0.81[ASN][1000 genomes]
rs285422	0.81[ASN][1000 genomes]
rs285435	0.93[ASN][1000 genomes]
rs285438	0.93[ASN][1000 genomes]
rs34201742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41267554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55890197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55957417	1.00[ASN][1000 genomes]
rs56201005	1.00[ASN][1000 genomes]
rs56277222	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57799548	0.95[ASN][1000 genomes]
rs58058936	1.00[ASN][1000 genomes]
rs6669449	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6696050	1.00[ASN][1000 genomes]
rs722260	0.97[ASN][1000 genomes]
rs72693816	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72693826	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74120755	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7521982	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7533908	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535829	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535979	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539622	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927844	0.90[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	nsv429902	chr1:165531342-165574342	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv946479	chr1:165549846-165553079	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165547400-165566800	Weak transcription	Psoas Muscle	Psoas
2	chr1:165549000-165551000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:165549600-165551200	Enhancers	NHEK	skin
4	chr1:165549600-165551600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:165549600-165551600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:165549800-165551600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:165550200-165551400	Enhancers	HMEC	breast
8	chr1:165550400-165551000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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