Variant report

Variant	rs12189724
Chromosome Location	chr6:2395218-2395219
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	chr6:2382708..2384223-chr6:2394952..2397063,2	MCF-7	breast:
2	chr6:2362511..2364691-chr6:2394137..2395852,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10458063	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10458138	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10458139	0.80[EUR][1000 genomes]
rs10458140	0.80[EUR][1000 genomes]
rs10458141	0.80[EUR][1000 genomes]
rs10458142	0.80[EUR][1000 genomes]
rs11242760	0.88[EUR][1000 genomes]
rs11242761	0.88[EUR][1000 genomes]
rs11242766	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11242769	0.83[EUR][1000 genomes]
rs11753825	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11758482	0.80[EUR][1000 genomes]
rs12189681	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12195877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196223	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12198593	1.00[YRI][hapmap]
rs12199363	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12199637	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12205452	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12206851	0.80[EUR][1000 genomes]
rs12209220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12209322	0.83[AMR][1000 genomes]
rs12209326	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12209801	0.90[EUR][1000 genomes]
rs12210286	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12210452	0.83[EUR][1000 genomes]
rs12213643	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525444	0.85[AFR][1000 genomes]
rs12525582	0.88[EUR][1000 genomes]
rs12526475	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12527624	0.89[EUR][1000 genomes]
rs12528202	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12529507	1.00[YRI][hapmap]
rs12662045	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13196348	0.85[AFR][1000 genomes]
rs13202573	1.00[YRI][hapmap]
rs13214014	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13214565	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073003	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2076470	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2294659	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34885387	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35144026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612673	0.88[EUR][1000 genomes]
rs3734506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3817904	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71552116	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71552117	0.88[EUR][1000 genomes]
rs764345	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9328099	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9503155	0.82[EUR][1000 genomes]
rs983027	0.83[EUR][1000 genomes]
rs983028	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
10	esv2763527	chr6:2390712-2400244	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2362400-2397200	Weak transcription	Liver	Liver
2	chr6:2362800-2397200	Weak transcription	Left Ventricle	heart
3	chr6:2381000-2397200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:2382800-2397000	Weak transcription	Fetal Stomach	stomach
5	chr6:2383000-2396800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:2383000-2397600	Weak transcription	Gastric	stomach
7	chr6:2383200-2398800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:2387000-2396800	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:2387600-2398200	Weak transcription	Ovary	ovary
10	chr6:2387800-2397400	Weak transcription	Adipose Nuclei	Adipose
11	chr6:2389400-2397600	Weak transcription	Pancreas	Pancrea
12	chr6:2389600-2396800	Weak transcription	Spleen	Spleen
13	chr6:2389600-2397200	Weak transcription	Lung	lung
14	chr6:2389600-2398600	Weak transcription	Esophagus	oesophagus
15	chr6:2390600-2399000	Weak transcription	Fetal Intestine Large	intestine
16	chr6:2391600-2399400	Weak transcription	Primary T cells from cord blood	blood
17	chr6:2392400-2400600	Weak transcription	Aorta	Aorta
18	chr6:2392400-2414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:2392800-2397600	Weak transcription	Fetal Intestine Small	intestine
20	chr6:2394400-2397600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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