Variant report

Variant	rs12058566
Chromosome Location	chr1:61725568-61725569
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	chr1:61711526..61714321-chr1:61724717..61727346,2	MCF-7	breast:
2	chr1:61724468..61727373-chr1:61734110..61737676,4	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11577416	0.95[EUR][1000 genomes]
rs12565984	0.82[ASN][1000 genomes]
rs17121853	0.83[CEU][hapmap];0.82[ASN][1000 genomes]
rs17377379	0.83[CEU][hapmap]
rs34351432	0.82[ASN][1000 genomes]
rs3737196	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs72664889	0.90[EUR][1000 genomes]
rs7540527	0.83[CEU][hapmap]

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	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS 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 target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61716000-61725600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:61719400-61737200	Weak transcription	Esophagus	oesophagus
3	chr1:61720800-61755800	Weak transcription	Fetal Intestine Small	intestine
4	chr1:61721000-61727000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:61721000-61732200	Weak transcription	Aorta	Aorta
6	chr1:61721000-61732800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:61721000-61754400	Weak transcription	Pancreas	Pancrea
8	chr1:61721200-61725600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:61721600-61727000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:61721600-61727200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:61721800-61727000	Weak transcription	Fetal Stomach	stomach
12	chr1:61721800-61728200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:61721800-61731000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:61721800-61732200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:61721800-61734400	Weak transcription	Small Intestine	intestine
16	chr1:61722800-61740600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:61724000-61726000	Enhancers	Brain Germinal Matrix	brain
18	chr1:61724400-61726000	Enhancers	Left Ventricle	heart
19	chr1:61724600-61726800	Weak transcription	Fetal Brain Male	brain
20	chr1:61724800-61726400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:61725000-61725800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:61725000-61725800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:61725000-61725800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:61725000-61726000	Enhancers	Adipose Nuclei	Adipose
25	chr1:61725000-61726000	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:61725000-61726000	Enhancers	Brain Hippocampus Middle	brain
27	chr1:61725000-61726000	Enhancers	Colon Smooth Muscle	Colon
28	chr1:61725000-61726000	Enhancers	Fetal Heart	heart
29	chr1:61725000-61726000	Enhancers	Fetal Muscle Leg	muscle
30	chr1:61725000-61726000	Enhancers	Right Ventricle	heart
31	chr1:61725000-61726000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:61725000-61726200	Enhancers	Psoas Muscle	Psoas
33	chr1:61725200-61725600	Enhancers	Brain Angular Gyrus	brain
34	chr1:61725200-61725600	Enhancers	Fetal Lung	lung
35	chr1:61725200-61725600	Weak transcription	Ovary	ovary
36	chr1:61725200-61725800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:61725200-61726000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr1:61725200-61726000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr1:61725200-61726000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:61725200-61726000	Enhancers	Liver	Liver
41	chr1:61725200-61726000	Enhancers	Brain Substantia Nigra	brain
42	chr1:61725200-61726200	Enhancers	Brain Anterior Caudate	brain
43	chr1:61725400-61725600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:61725400-61725800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:61725400-61725800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr1:61725400-61725800	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:61725400-61726000	Weak transcription	Right Atrium	heart
48	chr1:61725400-61727000	Weak transcription	Fetal Brain Female	brain
49	chr1:61725400-61727200	Weak transcription	HepG2	liver
50	chr1:61725400-61729000	Weak transcription	K562	blood

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