Variant report

Variant	rs12188905
Chromosome Location	chr5:92900435-92900436
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	chr5:92899115..92901267-chr5:92906370..92908951,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237187	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10041792	0.88[JPT][hapmap]
rs1004941	0.88[JPT][hapmap]
rs10050364	0.86[JPT][hapmap]
rs10051878	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10060331	0.86[JPT][hapmap]
rs10067541	0.88[JPT][hapmap]
rs10071040	0.88[JPT][hapmap]
rs1038686	0.86[JPT][hapmap]
rs1046217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10476520	0.88[JPT][hapmap]
rs10514376	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11135388	0.88[EUR][1000 genomes]
rs11951859	0.84[EUR][1000 genomes]
rs11952115	0.90[EUR][1000 genomes]
rs11952600	0.86[EUR][1000 genomes]
rs11960608	0.90[EUR][1000 genomes]
rs12186735	0.93[ASN][1000 genomes]
rs12187239	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188716	0.93[ASN][1000 genomes]
rs12188845	0.86[EUR][1000 genomes]
rs13154650	0.86[JPT][hapmap]
rs13161885	0.86[JPT][hapmap]
rs1370977	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457101	0.88[EUR][1000 genomes]
rs17082127	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17082129	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17083145	0.84[EUR][1000 genomes]
rs17083155	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17083181	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17083191	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083194	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083198	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083200	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083213	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083228	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17083297	0.86[JPT][hapmap]
rs17312456	0.86[JPT][hapmap]
rs17370695	0.93[ASN][1000 genomes]
rs1824153	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1844343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083227	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279473	0.93[ASN][1000 genomes]
rs2344387	0.86[EUR][1000 genomes]
rs3776601	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs55861967	0.84[EUR][1000 genomes]
rs57165666	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57690257	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59360932	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61324921	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61352323	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556823	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6556824	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556829	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6866771	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877616	0.86[JPT][hapmap]
rs6879816	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880843	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6884138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6889857	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890998	0.86[JPT][hapmap]
rs6895356	0.88[JPT][hapmap]
rs6898507	0.86[JPT][hapmap]
rs73133214	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133217	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133226	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73133228	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73133239	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73133251	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133254	0.84[EUR][1000 genomes]
rs73133258	0.86[EUR][1000 genomes]
rs73133261	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133265	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133275	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133278	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133280	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133282	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133283	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133287	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133289	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133292	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133301	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135313	0.86[EUR][1000 genomes]
rs73135320	0.93[ASN][1000 genomes]
rs73135321	0.93[ASN][1000 genomes]
rs73772907	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702348	0.88[JPT][hapmap]
rs7702649	0.86[JPT][hapmap]
rs7712388	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7712899	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715034	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7717718	0.88[JPT][hapmap]
rs7721168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7721509	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7727107	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736624	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9314086	0.86[JPT][hapmap]

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	nsv1022355	chr5:92846496-92911797	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
2	nsv537807	chr5:92846496-92911797	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
3	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv1819334	chr5:92892591-92956733	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv882383	chr5:92895401-92928346	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv823130	chr5:92896346-92966016	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv4918	chr5:92898426-92943359	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv823132	chr5:92898512-92969668	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92859200-92905000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:92859400-92905000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:92859400-92905600	Weak transcription	Placenta	Placenta
4	chr5:92860000-92908000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:92883200-92900800	Weak transcription	Fetal Brain Male	brain
6	chr5:92889400-92905400	Weak transcription	Fetal Brain Female	brain
7	chr5:92889600-92905800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:92889600-92909800	Weak transcription	Ovary	ovary
9	chr5:92890000-92904600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:92890600-92903200	Weak transcription	Brain Germinal Matrix	brain
11	chr5:92895400-92901400	Weak transcription	Brain Angular Gyrus	brain
12	chr5:92898400-92904400	Weak transcription	Fetal Stomach	stomach
13	chr5:92898600-92906000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:92899200-92906400	Weak transcription	HSMM	muscle
15	chr5:92899400-92900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:92899400-92902000	Weak transcription	Fetal Kidney	kidney
17	chr5:92899600-92901600	Weak transcription	Fetal Lung	lung
18	chr5:92899600-92904200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:92899800-92901000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:92899800-92901000	Enhancers	HMEC	breast
21	chr5:92899800-92901000	Enhancers	HUVEC	blood vessel
22	chr5:92899800-92901000	Enhancers	NH-A	brain
23	chr5:92899800-92901000	Enhancers	NHLF	lung
24	chr5:92899800-92901200	Enhancers	NHDF-Ad	bronchial
25	chr5:92899800-92905000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:92900200-92900600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:92900200-92900600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:92900200-92900600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:92900200-92900600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:92900200-92900600	Flanking Active TSS	Osteobl	bone
31	chr5:92900200-92900800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:92900200-92900800	Enhancers	Hela-S3	cervix
33	chr5:92900200-92900800	Enhancers	HSMMtube	muscle

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