Variant report

Variant	rs12239863
Chromosome Location	chr1:225838848-225838849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225837427..225840377-chr1:226110786..226113665,3	MCF-7	breast:
2	chr1:225837738..225841787-chr1:225965241..225967265,3	MCF-7	breast:
3	chr1:225838732..225840997-chr1:226248323..226251215,2	MCF-7	breast:
4	chr1:225811629..225814682-chr1:225837317..225840214,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4149227	1.00[LWK][hapmap]

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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:225825600-225839600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:225826200-225839400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:225830400-225839200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:225830400-225839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:225830400-225839600	Weak transcription	Gastric	stomach
7	chr1:225834200-225839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:225834800-225839200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:225836200-225839200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:225836200-225840400	Active TSS	Right Atrium	heart
11	chr1:225836200-225842000	Active TSS	Aorta	Aorta
12	chr1:225836600-225841400	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr1:225836600-225842200	Active TSS	Right Ventricle	heart
14	chr1:225836600-225842200	Active TSS	Stomach Smooth Muscle	stomach
15	chr1:225836800-225842200	Active TSS	NHLF	lung
16	chr1:225837000-225842000	Active TSS	Ovary	ovary
17	chr1:225837000-225842800	Active TSS	Psoas Muscle	Psoas
18	chr1:225837200-225839000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:225837200-225841800	Active TSS	Osteobl	bone
20	chr1:225837200-225842800	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:225837400-225839000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:225837400-225839200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:225837400-225842200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:225837600-225841600	Active TSS	Fetal Muscle Leg	muscle
25	chr1:225837600-225841800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:225837600-225842000	Active TSS	Fetal Lung	lung
27	chr1:225837600-225842000	Active TSS	Rectal Smooth Muscle	rectum
28	chr1:225837600-225842400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:225838000-225839200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:225838000-225841400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:225838000-225841800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:225838000-225841800	Active TSS	Colon Smooth Muscle	Colon
33	chr1:225838000-225842000	Active TSS	Fetal Stomach	stomach
34	chr1:225838000-225842200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:225838000-225842400	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr1:225838000-225842400	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr1:225838000-225842800	Active TSS	A549	lung
38	chr1:225838200-225839200	Active TSS	Adipose Nuclei	Adipose
39	chr1:225838200-225839200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:225838200-225839400	Active TSS	HepG2	liver
41	chr1:225838200-225839600	Active TSS	Brain Germinal Matrix	brain
42	chr1:225838200-225841600	Active TSS	Fetal Brain Female	brain
43	chr1:225838200-225841800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:225838200-225841800	Active TSS	Muscle Satellite Cultured Cells	--
45	chr1:225838200-225842000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:225838200-225842000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:225838200-225842000	Active TSS	NH-A	brain
48	chr1:225838200-225842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:225838200-225842200	Active TSS	HSMM	muscle
50	chr1:225838200-225842200	Active TSS	HSMMtube	muscle

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