Variant report

Variant	rs12588029
Chromosome Location	chr14:66108215-66108216
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	chr14:66107011..66108860-chr3:124216151..124218690,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10129187	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10129472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10129732	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10130560	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10133167	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10133902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10133903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10135594	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10135934	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10136412	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10136763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10143822	1.00[EUR][1000 genomes]
rs10145561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10145993	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10145996	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10146179	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10150052	0.83[ASN][1000 genomes]
rs10151921	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10162379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10162474	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10162506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10220303	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10220304	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10483779	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10483784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379147	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13379229	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17102686	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102757	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17102836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17102844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17102896	0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs17102920	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17779061	0.81[AMR][1000 genomes]
rs17779571	0.93[EUR][1000 genomes]
rs1813030	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1950559	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1953419	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1958562	1.00[CEU][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1959146	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1959147	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1959148	0.90[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2002691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2092915	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2411814	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2411818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2411819	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373922	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28390075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28427101	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28430347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28452027	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28694288	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28695252	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28823043	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28830595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28871950	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2898817	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2898819	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3783707	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4516142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45549535	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4600391	0.82[AMR][1000 genomes]
rs57638372	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58170348	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59970730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61987818	0.83[ASN][1000 genomes]
rs6573623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140251	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7141326	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7145319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7145834	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7148401	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7151690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7160505	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73270603	0.93[ASN][1000 genomes]
rs73270608	0.91[ASN][1000 genomes]
rs73284130	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73284149	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73284201	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8003664	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8012058	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8014146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015947	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8017901	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9323462	0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9323464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs945319	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9972109	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
5	esv3366524	chr14:65924360-66423862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1045000	chr14:66010886-66372518	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1042671	chr14:66010886-66399888	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv902026	chr14:66061020-66171541	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:66077600-66114400	Weak transcription	Ovary	ovary
2	chr14:66080800-66117600	Weak transcription	Left Ventricle	heart
3	chr14:66081400-66142200	Weak transcription	Thymus	Thymus
4	chr14:66081800-66112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr14:66082200-66112600	Weak transcription	NHDF-Ad	bronchial
6	chr14:66082800-66117600	Weak transcription	Aorta	Aorta
7	chr14:66086400-66119600	Weak transcription	Pancreas	Pancrea
8	chr14:66090800-66145000	Weak transcription	Small Intestine	intestine
9	chr14:66092800-66141000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr14:66098000-66116000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr14:66098000-66125000	Weak transcription	Brain Substantia Nigra	brain
12	chr14:66098200-66115200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr14:66098200-66118800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr14:66099000-66135200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr14:66099200-66115200	Weak transcription	Placenta	Placenta
16	chr14:66099200-66135800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr14:66099200-66144000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr14:66100600-66160000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:66103200-66112400	Weak transcription	Fetal Intestine Large	intestine
20	chr14:66104600-66115600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:66104600-66117200	Weak transcription	Fetal Intestine Small	intestine
22	chr14:66104800-66113200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr14:66104800-66116400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr14:66105000-66110800	Weak transcription	Dnd41	blood
25	chr14:66105000-66111600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr14:66105000-66112400	Weak transcription	Primary B cells from cord blood	blood
27	chr14:66105000-66112800	Weak transcription	Gastric	stomach
28	chr14:66105000-66117600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:66105000-66125000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr14:66105000-66143400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:66105000-66149600	Weak transcription	Fetal Thymus	thymus
32	chr14:66105000-66157400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr14:66105200-66110800	Weak transcription	GM12878-XiMat	blood
34	chr14:66105200-66111600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr14:66105200-66112800	Weak transcription	Primary T cells from cord blood	blood
36	chr14:66105200-66113200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr14:66105200-66117400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr14:66105200-66119000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr14:66105200-66120200	Weak transcription	NH-A	brain
40	chr14:66105200-66135600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr14:66105200-66136000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr14:66107000-66126400	Weak transcription	Stomach Mucosa	stomach
43	chr14:66108200-66108400	Enhancers	Brain Cingulate Gyrus	brain

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