Variant report

Variant	rs12062612
Chromosome Location	chr1:171189744-171189745
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	chr1:171187797..171189835-chr1:171191564..171194285,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225243	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10912559	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs10912597	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][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]
rs12354013	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12354030	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6661174	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs6664553	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs6671692	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs6672456	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs6701702	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs7054006	1.00[AMR][1000 genomes]
rs73030605	1.00[AMR][1000 genomes]
rs7517460	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs7536646	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs7536745	0.89[YRI][hapmap];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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171169800-171189800	Weak transcription	Right Atrium	heart
2	chr1:171183000-171189800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:171183400-171189800	Weak transcription	Left Ventricle	heart
4	chr1:171186800-171190200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:171186800-171190200	Enhancers	Placenta	Placenta
6	chr1:171187200-171190400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:171187400-171189800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:171187600-171190400	Enhancers	Stomach Mucosa	stomach
9	chr1:171187800-171189800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:171187800-171190000	Enhancers	Brain Hippocampus Middle	brain
11	chr1:171187800-171191400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:171188000-171189800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:171188000-171189800	Weak transcription	Psoas Muscle	Psoas
14	chr1:171188000-171192200	Weak transcription	Pancreas	Pancrea
15	chr1:171188600-171189800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:171188800-171190000	Enhancers	Aorta	Aorta
17	chr1:171188800-171190000	Enhancers	HSMM	muscle
18	chr1:171188800-171190200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:171189000-171189800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:171189000-171189800	Weak transcription	Brain Anterior Caudate	brain
21	chr1:171189000-171190000	Enhancers	Fetal Brain Male	brain
22	chr1:171189000-171190400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr1:171189000-171190400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:171189000-171191000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:171189000-171191600	Weak transcription	Small Intestine	intestine
26	chr1:171189200-171189800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr1:171189200-171189800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr1:171189200-171190000	Flanking Active TSS	HMEC	breast
29	chr1:171189200-171190000	Flanking Active TSS	Osteobl	bone
30	chr1:171189200-171190200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr1:171189200-171190200	Enhancers	Fetal Heart	heart
32	chr1:171189200-171190400	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr1:171189200-171190400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:171189200-171190400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:171189200-171190600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:171189200-171192600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:171189400-171189800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:171189400-171189800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:171189400-171189800	Flanking Active TSS	Fetal Stomach	stomach
40	chr1:171189400-171189800	Enhancers	NHEK	skin
41	chr1:171189400-171190000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:171189400-171190000	Flanking Active TSS	NH-A	brain
43	chr1:171189400-171190200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:171189400-171190200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:171189400-171190200	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr1:171189400-171190200	Flanking Active TSS	NHLF	lung
47	chr1:171189600-171189800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:171189600-171189800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:171189600-171189800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:171189600-171189800	Active TSS	Fetal Muscle Trunk	muscle

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