Variant report

Variant	rs12498291
Chromosome Location	chr4:129144145-129144146
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129142342..129144660-chr4:129149158..129151312,2	MCF-7	breast:
2	chr4:129143357..129145354-chr4:129208658..129211000,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164040	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10000960	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10002580	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10014664	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10025430	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10026123	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10026899	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10213259	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10434053	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10518529	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1064205	0.81[ASN][1000 genomes]
rs10857128	0.84[ASN][1000 genomes]
rs10857129	0.83[ASN][1000 genomes]
rs11098946	0.81[ASN][1000 genomes]
rs11098950	0.84[ASN][1000 genomes]
rs11098951	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11727305	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11728245	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11732074	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11735810	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11737026	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737508	0.81[ASN][1000 genomes]
rs11941199	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12505717	0.84[ASN][1000 genomes]
rs12506549	0.81[ASN][1000 genomes]
rs12507742	0.84[ASN][1000 genomes]
rs12508837	0.84[ASN][1000 genomes]
rs12509092	0.84[ASN][1000 genomes]
rs12510308	0.81[EUR][1000 genomes]
rs12641548	0.81[ASN][1000 genomes]
rs12645577	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13102049	0.81[ASN][1000 genomes]
rs13109815	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13138581	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13139182	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13139685	0.81[ASN][1000 genomes]
rs16997980	0.81[ASN][1000 genomes]
rs1809796	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1809797	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1870686	0.84[ASN][1000 genomes]
rs1870687	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1948506	0.80[EUR][1000 genomes]
rs1971933	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1975879	0.81[ASN][1000 genomes]
rs2061570	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2061571	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2100798	0.81[ASN][1000 genomes]
rs2100799	0.81[ASN][1000 genomes]
rs2172813	0.96[ASN][1000 genomes]
rs2204117	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306054	0.81[ASN][1000 genomes]
rs2306055	0.84[ASN][1000 genomes]
rs2391231	0.86[ASN][1000 genomes]
rs28625259	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34021656	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34350456	0.81[ASN][1000 genomes]
rs34503080	0.86[ASN][1000 genomes]
rs34658734	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34800130	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34816181	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34823354	0.84[ASN][1000 genomes]
rs35239105	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35636574	0.84[ASN][1000 genomes]
rs3733320	0.84[ASN][1000 genomes]
rs4383632	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4385082	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4484314	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4527494	0.84[ASN][1000 genomes]
rs4576015	0.83[ASN][1000 genomes]
rs4618332	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4833394	0.81[ASN][1000 genomes]
rs4833395	0.81[ASN][1000 genomes]
rs4834228	0.81[ASN][1000 genomes]
rs4834229	0.81[ASN][1000 genomes]
rs4834230	0.84[ASN][1000 genomes]
rs4834233	0.84[ASN][1000 genomes]
rs4834234	0.86[ASN][1000 genomes]
rs4975239	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55720227	0.97[ASN][1000 genomes]
rs55849105	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55912890	0.97[ASN][1000 genomes]
rs57137613	0.83[ASN][1000 genomes]
rs59944017	0.86[ASN][1000 genomes]
rs62321076	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62335638	0.81[ASN][1000 genomes]
rs62335645	0.82[ASN][1000 genomes]
rs62336165	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62336168	0.97[ASN][1000 genomes]
rs6534660	0.81[ASN][1000 genomes]
rs6534661	0.81[ASN][1000 genomes]
rs6534662	0.81[ASN][1000 genomes]
rs6534666	0.84[ASN][1000 genomes]
rs6534668	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6534669	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6534670	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6534672	0.92[EUR][1000 genomes]
rs6534673	0.92[EUR][1000 genomes]
rs6534674	0.80[EUR][1000 genomes]
rs6815163	0.86[ASN][1000 genomes]
rs6815890	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6816751	0.97[ASN][1000 genomes]
rs6818467	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6820515	0.83[ASN][1000 genomes]
rs6820831	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6829891	0.90[ASN][1000 genomes]
rs6834263	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6839370	0.84[ASN][1000 genomes]
rs6842281	0.86[ASN][1000 genomes]
rs6849546	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6849865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850479	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6851796	0.84[ASN][1000 genomes]
rs6851896	0.82[ASN][1000 genomes]
rs6856312	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7661888	0.83[ASN][1000 genomes]
rs7667562	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7667689	0.90[EUR][1000 genomes]
rs7669406	0.82[ASN][1000 genomes]
rs7671235	0.82[ASN][1000 genomes]
rs7671641	0.84[ASN][1000 genomes]
rs7684955	0.81[ASN][1000 genomes]
rs7688852	0.80[EUR][1000 genomes]
rs7691540	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7693135	0.90[ASN][1000 genomes]
rs7696130	0.81[ASN][1000 genomes]
rs9760910	0.84[ASN][1000 genomes]
rs9790488	0.81[ASN][1000 genomes]
rs9993435	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129108200-129149400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:129122800-129149000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:129123000-129144800	Weak transcription	Left Ventricle	heart
4	chr4:129123000-129145800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:129123000-129149000	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:129123000-129149400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:129128200-129149200	Weak transcription	Aorta	Aorta
8	chr4:129128400-129149000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:129129800-129149000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:129130800-129149600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:129133600-129149400	Weak transcription	Pancreas	Pancrea
12	chr4:129134400-129149200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:129135000-129149600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:129142000-129145800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:129142200-129145600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:129142200-129145800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:129142200-129145800	Weak transcription	HSMMtube	muscle
18	chr4:129143000-129145400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:129143000-129145400	Weak transcription	Osteobl	bone
20	chr4:129143000-129145800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:129143000-129146000	Weak transcription	HSMM	muscle
22	chr4:129143200-129144800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:129143200-129146000	Weak transcription	NH-A	brain
24	chr4:129143200-129146000	Weak transcription	NHDF-Ad	bronchial
25	chr4:129143200-129147200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:129143400-129145000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:129143600-129145600	Weak transcription	Fetal Heart	heart
28	chr4:129143600-129145800	Weak transcription	NHLF	lung
29	chr4:129143800-129145000	Strong transcription	Liver	Liver
30	chr4:129143800-129145000	Strong transcription	Fetal Intestine Small	intestine
31	chr4:129144000-129144400	Strong transcription	Fetal Stomach	stomach

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