Variant report

Variant	rs2309415
Chromosome Location	chr9:71897811-71897812
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	chr9:71893881..71896810-chr9:71896857..71898912,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10249	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10780246	0.81[AMR][1000 genomes]
rs10780251	0.83[AMR][1000 genomes]
rs10780256	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10780257	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10867253	0.81[AMR][1000 genomes]
rs10867330	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11137822	0.81[AMR][1000 genomes]
rs11137955	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1339544	1.00[ASW][hapmap]
rs1416737	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1538580	0.81[AMR][1000 genomes]
rs1538582	0.81[AMR][1000 genomes]
rs1890632	0.81[AMR][1000 genomes]
rs1890635	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890636	0.90[ASN][1000 genomes]
rs1890637	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890638	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890639	0.81[AMR][1000 genomes]
rs2095347	0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2095875	0.81[AMR][1000 genomes]
rs2105214	0.81[AMR][1000 genomes]
rs2309416	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2309417	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309419	0.82[AMR][1000 genomes]
rs2309429	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2309430	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4269598	0.86[ASN][1000 genomes]
rs4301505	0.88[ASN][1000 genomes]
rs4308798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4515616	1.00[ASW][hapmap]
rs4744865	0.81[AMR][1000 genomes]
rs4744870	0.90[ASN][1000 genomes]
rs4744871	0.90[ASN][1000 genomes]
rs4744872	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559403	0.81[AMR][1000 genomes]
rs6559404	0.81[AMR][1000 genomes]
rs7027248	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027671	1.00[ASW][hapmap]
rs7030339	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030477	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7861213	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs7868867	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription 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	26 gene(s)	inside rSNPs	diseases
5	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	esv1796249	chr9:71862129-71911566	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
11	esv1798130	chr9:71883224-71903309	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv1810420	chr9:71883224-71903309	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv1850866	chr9:71883224-71903309	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3481655	chr9:71893432-71898430	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv3495891	chr9:71894099-71898637	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3481654	chr9:71894157-71898005	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv3495894	chr9:71894182-71898180	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv1793672	chr9:71895608-71898527	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv1798976	chr9:71895608-71898527	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv1844413	chr9:71895608-71898527	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv614562	chr9:71895608-71898527	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv614563	chr9:71895608-71898969	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv614564	chr9:71895608-71903309	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv614565	chr9:71895608-71903717	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv614566	chr9:71895660-71898969	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv1817873	chr9:71895731-71898527	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv1832538	chr9:71895731-71898969	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv1836549	chr9:71895731-71898969	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2309415	FAM122A	cis	cerebellum	SCAN
rs2309415	FXN	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71895000-71898000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:71897400-71898400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:71897400-71899000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr9:71897400-71899000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:71897400-71899400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:71897600-71899000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr9:71897600-71899000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr9:71897800-71898200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:71897800-71898200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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