Variant report

Variant	rs12720686
Chromosome Location	chr1:186946631-186946632
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	chr1:186574674..186575283-chr1:186946255..186947085,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTGS2-2	chr1:186946565-186946634	NONHSAT008453

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12720615	1.00[EUR][1000 genomes]
rs12720672	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12720673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2383557	0.88[AFR][1000 genomes]
rs4650711	0.81[AFR][1000 genomes]
rs4650712	0.88[AFR][1000 genomes]
rs4650713	0.88[AFR][1000 genomes]
rs6672835	0.88[AFR][1000 genomes]
rs6674263	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv548407	chr1:186875459-186951429	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186881800-186951200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:186923400-186958800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:186926800-186951200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:186935000-186950800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:186935800-186947400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:186936000-186949400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:186936200-186948000	Weak transcription	Hela-S3	cervix
8	chr1:186936600-186947000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:186939200-186950000	Weak transcription	A549	lung
10	chr1:186939800-186947600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:186943400-186946800	Enhancers	NH-A	brain
12	chr1:186943400-186947200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:186943600-186948400	Enhancers	Colon Smooth Muscle	Colon
14	chr1:186943600-186948400	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:186943800-186948400	Enhancers	NHDF-Ad	bronchial
16	chr1:186944000-186947600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:186944200-186946800	Enhancers	Stomach Smooth Muscle	stomach
18	chr1:186944200-186947800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:186944400-186947400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:186944400-186951600	Weak transcription	Adipose Nuclei	Adipose
21	chr1:186944600-186946800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:186944800-186947000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:186945000-186947600	Weak transcription	Osteobl	bone
24	chr1:186945000-186948000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:186945000-186949200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:186945000-186952200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:186945200-186947200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:186945800-186947600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:186946000-186948000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:186946000-186948000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:186946200-186951200	Weak transcription	Fetal Stomach	stomach
32	chr1:186946400-186947000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:186946400-186947000	Enhancers	HMEC	breast
34	chr1:186946400-186948400	Flanking Active TSS	HUVEC	blood vessel
35	chr1:186946600-186946800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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