Variant report

Variant	rs12078939
Chromosome Location	chr1:186083536-186083537
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186080718..186085841-chr1:186086929..186090356,5	MCF-7	breast:
2	chr1:186072627..186074897-chr1:186081775..186084159,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10157742	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10157924	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1022670	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1022671	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489755	0.82[ASN][1000 genomes]
rs10489756	0.83[ASN][1000 genomes]
rs10752960	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10752961	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10752962	0.83[ASN][1000 genomes]
rs10798035	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798036	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10798037	0.80[ASN][1000 genomes]
rs10911810	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911811	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10911812	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911813	0.87[ASN][1000 genomes]
rs10911814	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10911815	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10911816	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10911819	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911820	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911825	0.80[ASN][1000 genomes]
rs10911826	0.80[ASN][1000 genomes]
rs12061689	0.80[ASN][1000 genomes]
rs12080760	0.80[ASN][1000 genomes]
rs12122227	0.83[ASN][1000 genomes]
rs12124204	0.81[ASN][1000 genomes]
rs12565788	0.82[ASN][1000 genomes]
rs1555495	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1590273	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1830627	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1853249	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1923460	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1998088	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2038601	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057387	0.82[ASN][1000 genomes]
rs2057388	0.83[ASN][1000 genomes]
rs2064789	0.80[ASN][1000 genomes]
rs2064790	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2073308	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146098	0.82[ASN][1000 genomes]
rs2180480	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2224575	0.80[ASN][1000 genomes]
rs2383430	0.81[EUR][1000 genomes]
rs2383431	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2383432	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2383433	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2891228	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2891229	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3845367	0.80[ASN][1000 genomes]
rs4233125	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4535962	0.80[ASN][1000 genomes]
rs4650694	0.83[ASN][1000 genomes]
rs4650695	0.80[ASN][1000 genomes]
rs4651295	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651297	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651298	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651299	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4651300	0.85[ASN][1000 genomes]
rs6425015	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425016	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425017	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6659783	0.81[ASN][1000 genomes]
rs6673390	0.81[ASN][1000 genomes]
rs6687977	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689111	0.81[ASN][1000 genomes]
rs6696910	0.81[ASN][1000 genomes]
rs6698064	0.83[ASN][1000 genomes]
rs6701244	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702313	0.83[ASN][1000 genomes]
rs6703518	0.83[ASN][1000 genomes]
rs716755	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs716756	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720971	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs720972	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs721153	0.83[ASN][1000 genomes]
rs7511761	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7512168	0.81[ASN][1000 genomes]
rs7527490	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530133	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543494	0.89[ASN][1000 genomes]
rs7549552	0.80[ASN][1000 genomes]
rs7550425	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7552198	0.83[ASN][1000 genomes]
rs7552781	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555520	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555906	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761903	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs761904	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs761905	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9286859	0.80[ASN][1000 genomes]
rs9286860	0.80[ASN][1000 genomes]
rs970578	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs975398	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186046400-186135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:186052200-186118200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:186057400-186083800	Weak transcription	Adipose Nuclei	Adipose
4	chr1:186064000-186094200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:186064600-186092000	Weak transcription	Left Ventricle	heart
6	chr1:186064600-186113200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:186065200-186093800	Weak transcription	Spleen	Spleen
8	chr1:186072200-186091000	Weak transcription	NHDF-Ad	bronchial
9	chr1:186072600-186108400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:186072800-186107800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:186073000-186121400	Weak transcription	NH-A	brain
12	chr1:186075000-186113600	Weak transcription	Lung	lung
13	chr1:186076400-186106800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:186076800-186097200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:186079000-186108000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:186079200-186092000	Weak transcription	Liver	Liver
17	chr1:186079800-186087800	Weak transcription	Fetal Lung	lung
18	chr1:186080400-186121400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:186082000-186090200	Weak transcription	Aorta	Aorta
20	chr1:186082200-186083600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:186082200-186085600	Weak transcription	K562	blood
22	chr1:186082400-186090800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:186082800-186093800	Weak transcription	Ovary	ovary

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