Variant report

Variant	rs12894053
Chromosome Location	chr14:64353440-64353441
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	chr14:64350600..64353514-chr7:30543619..30546570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006625	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11158512	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11158516	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12435958	0.80[CEU][hapmap]
rs12587472	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12588087	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12894864	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1953241	0.90[JPT][hapmap]
rs1959034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1959035	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2150291	0.85[CHB][hapmap]
rs2210650	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275018	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357001	0.80[CEU][hapmap];0.80[AFR][1000 genomes]
rs2357002	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2357003	0.91[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34780876	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902247	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902248	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6573534	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7145657	0.85[ASN][1000 genomes]
rs7146821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7149766	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7153101	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7157314	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7157323	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7158974	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7160127	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7493416	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8005899	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8015158	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015354	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8022917	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945030	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs954730	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9707224	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs998241	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv564904	chr14:64346190-64416898	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1793389	chr14:64346190-64457224	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr14:64327600-64360000	Weak transcription	Gastric	stomach
3	chr14:64331200-64356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:64335200-64360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:64336800-64362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:64337000-64357200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr14:64337000-64365200	Weak transcription	Fetal Thymus	thymus
8	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
9	chr14:64338000-64353800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:64338000-64355200	Weak transcription	Primary B cells from cord blood	blood
11	chr14:64339400-64366800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr14:64341000-64356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr14:64341000-64357200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:64341200-64354000	Weak transcription	Dnd41	blood
15	chr14:64341200-64354800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr14:64341200-64356400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr14:64341200-64356400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr14:64341200-64356600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr14:64341200-64357000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:64341200-64357200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr14:64341200-64357200	Weak transcription	Fetal Lung	lung
22	chr14:64341200-64357200	Weak transcription	Fetal Muscle Leg	muscle
23	chr14:64341400-64356600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr14:64341400-64356600	Weak transcription	Fetal Kidney	kidney
25	chr14:64341400-64366800	Weak transcription	Primary T cells from cord blood	blood
26	chr14:64342400-64354800	Weak transcription	Aorta	Aorta
27	chr14:64342400-64357200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:64342600-64357400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:64342800-64354200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr14:64342800-64357000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr14:64342800-64357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:64342800-64360400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr14:64342800-64360400	Weak transcription	Hela-S3	cervix
34	chr14:64342800-64368400	Weak transcription	Esophagus	oesophagus
35	chr14:64343600-64359400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr14:64344400-64356600	Weak transcription	GM12878-XiMat	blood
39	chr14:64344400-64357000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr14:64344400-64357400	Weak transcription	Fetal Intestine Large	intestine
41	chr14:64344600-64357200	Weak transcription	HMEC	breast
42	chr14:64344800-64357200	Weak transcription	Small Intestine	intestine
43	chr14:64345000-64356800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr14:64345000-64357200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr14:64345000-64357200	Weak transcription	Ovary	ovary
46	chr14:64345000-64357200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr14:64345200-64354600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:64345200-64357200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr14:64345800-64357200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr14:64346600-64357200	Weak transcription	Fetal Brain Female	brain

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