Variant report

Variant	rs12685541
Chromosome Location	chr9:25413761-25413762
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	chr9:25408828..25410955-chr9:25413147..25416054,3	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10115498	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10115746	0.82[EUR][1000 genomes]
rs10119099	0.81[EUR][1000 genomes]
rs10119894	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10121903	0.81[EUR][1000 genomes]
rs10733401	0.82[EUR][1000 genomes]
rs10733402	0.82[EUR][1000 genomes]
rs10738716	0.82[EUR][1000 genomes]
rs10738717	0.82[EUR][1000 genomes]
rs10738718	0.82[EUR][1000 genomes]
rs10738719	0.82[EUR][1000 genomes]
rs10738720	0.85[AMR][1000 genomes]
rs10738721	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757522	0.82[EUR][1000 genomes]
rs10757523	0.82[EUR][1000 genomes]
rs10757524	0.81[EUR][1000 genomes]
rs10757525	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757526	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10757527	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757528	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757529	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757531	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757532	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757533	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10757536	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10757538	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10757539	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10757540	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10812228	0.83[AFR][1000 genomes]
rs10812233	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10812234	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10966883	0.83[EUR][1000 genomes]
rs10966884	0.82[EUR][1000 genomes]
rs10966885	0.82[EUR][1000 genomes]
rs10966887	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10966893	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10966896	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10966897	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377312	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1327380	0.82[EUR][1000 genomes]
rs1327381	0.82[EUR][1000 genomes]
rs1327382	0.82[EUR][1000 genomes]
rs1327383	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1327394	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409946	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1576030	0.81[ASN][1000 genomes]
rs1576040	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1590674	0.82[EUR][1000 genomes]
rs1616954	0.85[CEU][hapmap]
rs1668978	0.84[CEU][hapmap]
rs1831079	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1901324	0.82[EUR][1000 genomes]
rs1901325	0.82[EUR][1000 genomes]
rs1901326	0.80[EUR][1000 genomes]
rs1901327	0.82[EUR][1000 genomes]
rs1901328	0.82[EUR][1000 genomes]
rs1998961	0.82[EUR][1000 genomes]
rs1998962	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2025826	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2031736	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4384070	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4449878	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4480194	0.82[EUR][1000 genomes]
rs7019841	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7019892	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7026882	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7040844	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7040859	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7041045	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7468705	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7850662	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7850668	0.91[EUR][1000 genomes]
rs7850910	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7851064	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7855132	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7867884	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7868012	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7871092	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943510	0.82[EUR][1000 genomes]
rs945811	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv466309	chr9:25157678-25683220	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv613889	chr9:25157678-25683220	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1018570	chr9:25170659-25633419	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv540100	chr9:25170659-25633419	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv869035	chr9:25287213-25779281	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1033677	chr9:25325400-25583227	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv540101	chr9:25325400-25583227	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv531597	chr9:25325401-25779422	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv892824	chr9:25363830-25426760	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25396800-25415200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:25410600-25413800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:25410800-25414200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:25411000-25414200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:25411000-25415200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr9:25411200-25413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:25412600-25413800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr9:25412800-25415400	Weak transcription	Fetal Brain Male	brain
9	chr9:25413000-25414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:25413000-25416200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr9:25413200-25415200	Weak transcription	Brain Germinal Matrix	brain

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