Variant report

Variant	rs12066006
Chromosome Location	chr1:61802286-61802287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:61679578..61681382-chr1:61802246..61804281,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11207728	0.93[ASN][1000 genomes]
rs1125778	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12134760	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741051	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758060	0.96[ASN][1000 genomes]
rs1344420	0.93[ASN][1000 genomes]
rs1344421	0.93[ASN][1000 genomes]
rs1474873	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2103882	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2180198	0.93[ASN][1000 genomes]
rs2180199	0.93[ASN][1000 genomes]
rs2180200	0.93[ASN][1000 genomes]
rs2207788	0.93[ASN][1000 genomes]
rs2364467	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2886080	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4406666	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4915735	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4915737	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587917	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587918	0.93[ASN][1000 genomes]
rs6587919	0.90[ASN][1000 genomes]
rs6587920	0.93[ASN][1000 genomes]
rs6587921	0.93[ASN][1000 genomes]
rs6662305	0.93[ASN][1000 genomes]
rs6673795	0.93[ASN][1000 genomes]
rs6674884	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697762	0.93[ASN][1000 genomes]
rs6697777	0.93[ASN][1000 genomes]
rs6697913	0.90[ASN][1000 genomes]
rs6697955	0.90[ASN][1000 genomes]
rs7512491	0.93[ASN][1000 genomes]
rs7526670	0.93[ASN][1000 genomes]
rs7553582	0.93[ASN][1000 genomes]
rs9436206	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9436635	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436637	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61784800-61802800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:61784800-61803200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:61784800-61803600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:61785000-61802400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:61785000-61802400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:61786000-61813600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:61788400-61802800	Weak transcription	Placenta	Placenta
8	chr1:61790000-61803600	Weak transcription	Hela-S3	cervix
9	chr1:61790000-61805400	Weak transcription	Lung	lung
10	chr1:61796000-61803600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:61796200-61802400	Weak transcription	A549	lung
12	chr1:61796200-61805400	Weak transcription	Esophagus	oesophagus
13	chr1:61798400-61802600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:61798600-61805000	Enhancers	Fetal Heart	heart
15	chr1:61799200-61802800	Weak transcription	Fetal Kidney	kidney
16	chr1:61799600-61802600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:61799800-61802400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:61799800-61803600	Enhancers	Fetal Brain Female	brain
19	chr1:61800000-61802800	Weak transcription	Psoas Muscle	Psoas
20	chr1:61800000-61803000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:61800200-61804400	Enhancers	Brain Germinal Matrix	brain
22	chr1:61800400-61803400	Enhancers	Brain Anterior Caudate	brain
23	chr1:61800400-61803600	Enhancers	Brain Substantia Nigra	brain
24	chr1:61800400-61804000	Enhancers	Liver	Liver
25	chr1:61800800-61802600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:61800800-61802600	Weak transcription	NHEK	skin
27	chr1:61800800-61802800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:61800800-61802800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:61800800-61803400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:61800800-61803400	Weak transcription	Stomach Mucosa	stomach
31	chr1:61800800-61803600	Weak transcription	Small Intestine	intestine
32	chr1:61801000-61802400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:61801000-61802400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:61801000-61802600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:61801000-61802800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:61801000-61802800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:61801000-61802800	Weak transcription	Ovary	ovary
38	chr1:61801000-61803400	Weak transcription	Aorta	Aorta
39	chr1:61801000-61803400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:61801000-61805400	Weak transcription	Pancreas	Pancrea
41	chr1:61801000-61818600	Weak transcription	K562	blood
42	chr1:61801200-61802400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:61801200-61802400	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:61801200-61802600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:61801200-61802600	Weak transcription	Adipose Nuclei	Adipose
46	chr1:61801200-61802600	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:61801200-61802600	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:61801200-61802600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:61801200-61802800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:61801200-61802800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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