Variant report

Variant	rs1972650
Chromosome Location	chr5:61338444-61338445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:61334280..61336026-chr5:61338071..61340993,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10058486	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10062059	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10214027	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13175940	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13177362	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13178972	0.83[EUR][1000 genomes]
rs13180268	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1445884	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1445886	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1816097	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1816098	0.82[EUR][1000 genomes]
rs1820157	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1820159	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1833868	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1833871	0.83[EUR][1000 genomes]
rs1972651	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032875	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2032876	0.81[EUR][1000 genomes]
rs2166371	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2342989	0.97[ASN][1000 genomes]
rs2342990	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342991	0.83[EUR][1000 genomes]
rs3843448	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4235489	0.82[EUR][1000 genomes]
rs4273560	0.97[ASN][1000 genomes]
rs4273561	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4301180	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4337809	0.97[ASN][1000 genomes]
rs4407583	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4470716	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4699996	0.81[EUR][1000 genomes]
rs4699997	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699999	0.82[EUR][1000 genomes]
rs4700455	0.81[EUR][1000 genomes]
rs4700456	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700457	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700463	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449573	0.82[EUR][1000 genomes]
rs6449577	0.83[EUR][1000 genomes]
rs6869741	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6874917	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896815	0.82[EUR][1000 genomes]
rs7712508	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7734412	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7736993	0.82[EUR][1000 genomes]
rs867492	0.82[EUR][1000 genomes]
rs889275	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs918616	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9291745	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968159	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885479	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020693	chr5:61098865-61357032	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv881725	chr5:61265820-61376320	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv508363	chr5:61287078-61362885	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv830317	chr5:61298840-61478113	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1972650	C5orf44	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61333800-61347600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:61337000-61338600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
3	chr5:61337000-61339400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:61337000-61340200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr5:61337200-61338600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr5:61337200-61338600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
7	chr5:61337200-61338800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr5:61337200-61339000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:61337400-61338800	Enhancers	H9 Cell Line	embryonic stem cell
10	chr5:61337800-61340200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:61338000-61338800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:61338200-61338600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
13	chr5:61338200-61339200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:61338200-61340200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:61338400-61338600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell

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