Variant report

Variant	rs12354030
Chromosome Location	chr1:171187703-171187704
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	chr1:171182864..171185763-chr1:171186408..171189341,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10912559	1.00[AMR][1000 genomes]
rs10912597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062612	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064360	0.83[AFR][1000 genomes]
rs12070707	1.00[AMR][1000 genomes]
rs12072582	1.00[AMR][1000 genomes]
rs12073562	1.00[AMR][1000 genomes]
rs12082524	1.00[AMR][1000 genomes]
rs12098211	0.83[AFR][1000 genomes]
rs12354013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6661174	1.00[AMR][1000 genomes]
rs6664553	1.00[AMR][1000 genomes]
rs6671692	1.00[AMR][1000 genomes]
rs6672456	1.00[AMR][1000 genomes]
rs6701702	1.00[AMR][1000 genomes]
rs7054006	1.00[AMR][1000 genomes]
rs73030605	1.00[AMR][1000 genomes]
rs7517460	1.00[AMR][1000 genomes]
rs7536646	1.00[AMR][1000 genomes]
rs7536745	1.00[AMR][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171167200-171187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:171169800-171189800	Weak transcription	Right Atrium	heart
3	chr1:171179800-171187800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:171181000-171187800	Weak transcription	Fetal Lung	lung
5	chr1:171182800-171187800	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:171183000-171189800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:171183400-171189800	Weak transcription	Left Ventricle	heart
8	chr1:171183600-171187800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:171184000-171187800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:171184200-171187800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:171185400-171189000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:171185800-171189200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:171186600-171189000	Enhancers	NHEK	skin
14	chr1:171186600-171189200	Enhancers	HMEC	breast
15	chr1:171186800-171188800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:171186800-171189200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:171186800-171189600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:171186800-171190200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:171186800-171190200	Enhancers	Placenta	Placenta
20	chr1:171187000-171188000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr1:171187000-171189200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:171187200-171188000	Enhancers	Aorta	Aorta
23	chr1:171187200-171188000	Enhancers	Fetal Muscle Trunk	muscle
24	chr1:171187200-171188000	Enhancers	Gastric	stomach
25	chr1:171187200-171188800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:171187200-171189600	Enhancers	Adipose Nuclei	Adipose
27	chr1:171187200-171190400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:171187400-171187800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:171187400-171188000	Enhancers	Fetal Muscle Leg	muscle
30	chr1:171187400-171188600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:171187400-171188800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:171187400-171189800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:171187600-171187800	Weak transcription	Psoas Muscle	Psoas
34	chr1:171187600-171188000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:171187600-171188000	Enhancers	Pancreas	Pancrea
36	chr1:171187600-171188800	Enhancers	Brain Substantia Nigra	brain
37	chr1:171187600-171189200	Enhancers	Osteobl	bone
38	chr1:171187600-171189400	Enhancers	Fetal Stomach	stomach
39	chr1:171187600-171189600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:171187600-171190400	Enhancers	Stomach Mucosa	stomach

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