Variant report

Variant	rs2475354
Chromosome Location	chr9:10268794-10268795
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:10045409..10046174-chr9:10268540..10269128,2	MCF-7	breast:
2	chr9:10232139..10232838-chr9:10268581..10269404,3	MCF-7	breast:
3	chr9:10060352..10060896-chr9:10268535..10269397,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10733204	0.85[EUR][1000 genomes]
rs10959000	0.88[JPT][hapmap]
rs1322154	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1323501	0.85[EUR][1000 genomes]
rs1575257	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1575258	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16925631	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs16925679	0.82[JPT][hapmap]
rs1951786	0.85[EUR][1000 genomes]
rs2475327	0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2475328	0.83[AMR][1000 genomes]
rs2475330	0.86[AMR][1000 genomes]
rs2475331	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2475332	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2475333	0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs2475334	1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2475336	0.81[EUR][1000 genomes]
rs2475337	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2475338	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2475340	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2475341	0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2475342	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2475343	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2475345	0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2475346	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2475347	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2475348	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2475350	0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2475352	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475355	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2498609	1.00[MEX][hapmap]
rs2498611	0.90[MEX][hapmap]
rs2498614	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2498616	0.86[AMR][1000 genomes]
rs2498619	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2498620	0.81[EUR][1000 genomes]
rs2498621	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2498622	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2498623	0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2498625	0.82[LWK][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2498626	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2498627	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2498628	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2498629	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2498630	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2498631	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869963	0.85[EUR][1000 genomes]
rs9298653	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034731	chr9:9776126-10481262	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv892295	chr9:9832245-10380406	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1030657	chr9:10002355-10481262	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1033178	chr9:10169848-10428731	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv471280	chr9:10172572-10277602	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv466158	chr9:10172573-10277602	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv613375	chr9:10172573-10277602	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2758179	chr9:10188450-10370398	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv2759666	chr9:10188450-10370398	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv892310	chr9:10197122-10279606	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv892312	chr9:10231178-10279606	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv2753898	chr9:10251400-10276700	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv2762791	chr9:10253852-10325264	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1018748	chr9:10254793-10325252	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1033188	chr9:10255910-10325252	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv892313	chr9:10258040-10311000	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv892314	chr9:10260263-10279606	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1025315	chr9:10261734-10325252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:10264200-10271600	Weak transcription	Pancreas	Pancrea
2	chr9:10265600-10269000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:10266000-10269200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:10268400-10269200	Enhancers	HMEC	breast
5	chr9:10268600-10268800	Active TSS	Brain Hippocampus Middle	brain
6	chr9:10268600-10269000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:10268600-10269000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:10268600-10269000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:10268600-10269000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:10268600-10269000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:10268600-10269000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:10268600-10269000	Flanking Active TSS	Liver	Liver
13	chr9:10268600-10269000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr9:10268600-10269000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr9:10268600-10269000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr9:10268600-10269000	Flanking Active TSS	Fetal Lung	lung
17	chr9:10268600-10269000	Flanking Active TSS	HUVEC	blood vessel
18	chr9:10268600-10269000	Enhancers	NH-A	brain
19	chr9:10268600-10269200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:10268600-10269200	Enhancers	Aorta	Aorta
21	chr9:10268600-10269400	Enhancers	NHEK	skin
22	chr9:10268600-10269600	Enhancers	Fetal Heart	heart

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