Variant report

Variant	rs12066028
Chromosome Location	chr1:174260404-174260405
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174257821..174260787-chr1:174268762..174270773,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10489257	1.00[EUR][1000 genomes]
rs10912725	1.00[EUR][1000 genomes]
rs10912742	1.00[EUR][1000 genomes]
rs10912743	1.00[EUR][1000 genomes]
rs10912744	1.00[EUR][1000 genomes]
rs10912748	1.00[EUR][1000 genomes]
rs10912760	1.00[EUR][1000 genomes]
rs10912767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912768	1.00[EUR][1000 genomes]
rs10912783	1.00[EUR][1000 genomes]
rs10912784	1.00[EUR][1000 genomes]
rs10912785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12057220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12058498	1.00[EUR][1000 genomes]
rs12059051	1.00[EUR][1000 genomes]
rs12059636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059902	1.00[EUR][1000 genomes]
rs12067445	1.00[EUR][1000 genomes]
rs12069450	1.00[EUR][1000 genomes]
rs12070328	1.00[EUR][1000 genomes]
rs12071243	1.00[EUR][1000 genomes]
rs12073453	1.00[EUR][1000 genomes]
rs12075085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075263	1.00[EUR][1000 genomes]
rs12075962	1.00[EUR][1000 genomes]
rs12076425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12077462	1.00[EUR][1000 genomes]
rs12078222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079274	1.00[EUR][1000 genomes]
rs12081444	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12081595	1.00[EUR][1000 genomes]
rs12082017	1.00[EUR][1000 genomes]
rs12083355	1.00[EUR][1000 genomes]
rs12084911	1.00[EUR][1000 genomes]
rs12090908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12092291	1.00[EUR][1000 genomes]
rs12094140	1.00[EUR][1000 genomes]
rs12094364	1.00[EUR][1000 genomes]
rs12096013	1.00[EUR][1000 genomes]
rs12096718	1.00[EUR][1000 genomes]
rs12354281	1.00[EUR][1000 genomes]
rs1467397	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1956522	1.00[EUR][1000 genomes]
rs6659951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6673147	1.00[EUR][1000 genomes]
rs6682041	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv872554	chr1:174209978-174291950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174214600-174270000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:174232600-174262000	Weak transcription	HMEC	breast
3	chr1:174238200-174261200	Weak transcription	Hela-S3	cervix
4	chr1:174239600-174262400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:174240000-174270600	Weak transcription	Colonic Mucosa	Colon
6	chr1:174241000-174261600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:174242800-174277200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:174243800-174275800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:174244400-174274000	Weak transcription	Fetal Heart	heart
10	chr1:174246200-174284200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:174248200-174262200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:174248800-174265000	Weak transcription	Small Intestine	intestine
13	chr1:174249800-174262400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:174249800-174270000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:174250000-174260600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:174250600-174270200	Weak transcription	Psoas Muscle	Psoas
17	chr1:174251000-174262000	Weak transcription	Placenta	Placenta
18	chr1:174251200-174275800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:174251400-174270000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:174251400-174270000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:174251400-174276000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:174254600-174262200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:174256600-174262000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:174256800-174261400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr1:174257000-174261000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
26	chr1:174257000-174263200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:174257200-174260600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:174258200-174260600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr1:174258200-174260800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
30	chr1:174258400-174261400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:174258600-174261400	Strong transcription	Primary B cells from cord blood	blood
32	chr1:174258800-174261000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:174259400-174264600	Weak transcription	Right Atrium	heart
34	chr1:174259400-174265000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:174259400-174266400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:174259400-174270000	Weak transcription	Thymus	Thymus
37	chr1:174259400-174270200	Weak transcription	Gastric	stomach
38	chr1:174259600-174260600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:174259600-174261000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:174259600-174261600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:174259600-174266600	Weak transcription	Left Ventricle	heart
42	chr1:174259600-174267000	Weak transcription	Right Ventricle	heart
43	chr1:174259600-174270000	Weak transcription	Aorta	Aorta
44	chr1:174259600-174272200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:174259600-174276200	Weak transcription	Brain Anterior Caudate	brain
46	chr1:174259600-174277800	Weak transcription	K562	blood
47	chr1:174259800-174261000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:174259800-174262400	Weak transcription	Primary T cells from cord blood	blood
49	chr1:174259800-174270200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:174259800-174273800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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