Variant report

Variant	rs12891438
Chromosome Location	chr14:39499500-39499501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39457540..39460115-chr14:39498272..39500421,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1028591	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1040836	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12882909	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12883114	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12883946	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12887605	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12891260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12895569	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12896384	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896963	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12897263	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12897593	0.88[ASN][1000 genomes]
rs17607605	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17616347	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17617123	0.83[ASN][1000 genomes]
rs17617289	0.83[ASN][1000 genomes]
rs17670531	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17676972	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17679493	0.81[ASN][1000 genomes]
rs1884383	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884386	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1950508	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1960796	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2144526	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2144527	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273315	0.91[ASN][1000 genomes]
rs2415533	0.85[ASN][1000 genomes]
rs28364834	0.89[ASN][1000 genomes]
rs34292075	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34328534	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34870044	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34896803	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34984050	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35006421	0.81[ASN][1000 genomes]
rs35395604	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35412542	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35534904	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35729735	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35873738	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35976812	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4555056	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55902358	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55993688	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57550673	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59881143	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61338087	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6571887	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67190795	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7140282	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71407778	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7143056	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7143370	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7144730	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145712	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7151407	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7152392	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7154223	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs743222	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7493678	0.80[EUR][1000 genomes]
rs8007028	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8007240	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8011494	0.81[ASN][1000 genomes]
rs8017648	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8020013	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8020321	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9743466	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9743749	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39487200-39508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr14:39493400-39505800	Weak transcription	Psoas Muscle	Psoas
3	chr14:39495400-39505000	Weak transcription	Small Intestine	intestine
4	chr14:39495400-39505800	Weak transcription	Fetal Kidney	kidney
5	chr14:39495400-39518200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr14:39495600-39509800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:39495800-39516000	Weak transcription	Stomach Mucosa	stomach
8	chr14:39496000-39514800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:39496000-39520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:39496400-39499600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr14:39496600-39499600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:39496600-39500000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr14:39496600-39507800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr14:39497200-39500000	Strong transcription	HUVEC	blood vessel
15	chr14:39497400-39503200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:39497400-39506000	Weak transcription	Fetal Heart	heart
17	chr14:39497400-39518000	Strong transcription	HSMM	muscle
18	chr14:39497400-39519200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr14:39497600-39499800	Strong transcription	A549	lung
20	chr14:39497600-39501000	Weak transcription	Hela-S3	cervix
21	chr14:39497600-39507600	Weak transcription	Brain Germinal Matrix	brain
22	chr14:39497800-39499600	Weak transcription	Primary B cells from cord blood	blood
23	chr14:39497800-39500200	Strong transcription	Colonic Mucosa	Colon
24	chr14:39497800-39500600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:39497800-39500600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:39497800-39502400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr14:39497800-39505800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr14:39497800-39520400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:39497800-39521200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:39498000-39499600	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:39498000-39499600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr14:39498000-39500200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr14:39498000-39500200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr14:39498000-39501000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr14:39498000-39502000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:39498000-39502200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:39498000-39505800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr14:39498000-39510000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:39498000-39518400	Strong transcription	Osteobl	bone
40	chr14:39498000-39518600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr14:39498000-39524200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:39498200-39499800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr14:39498200-39499800	Strong transcription	Brain Substantia Nigra	brain
44	chr14:39498200-39501000	Strong transcription	Primary T cells from cord blood	blood
45	chr14:39498200-39502800	Strong transcription	HMEC	breast
46	chr14:39498200-39507600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:39498200-39509400	Weak transcription	Fetal Brain Male	brain
48	chr14:39498200-39510200	Strong transcription	Placenta	Placenta
49	chr14:39498200-39519400	Strong transcription	NH-A	brain
50	chr14:39498200-39524200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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