Variant report

Variant	rs12039453
Chromosome Location	chr1:225837690-225837691
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	chr1:225837427..225840377-chr1:226110786..226113665,3	MCF-7	breast:
2	chr1:225811629..225814682-chr1:225837317..225840214,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10429871	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11801322	0.86[EUR][1000 genomes]
rs12027872	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12033453	0.93[ASN][1000 genomes]
rs12038461	0.84[ASN][1000 genomes]
rs12038893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12043837	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1340868	1.00[TSI][hapmap]
rs16845078	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs16845153	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs17500814	1.00[TSI][hapmap]
rs17501138	1.00[TSI][hapmap]
rs17501956	1.00[TSI][hapmap]
rs17502068	1.00[TSI][hapmap]
rs17502774	0.82[EUR][1000 genomes]
rs17502823	0.88[EUR][1000 genomes]
rs17502858	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17502961	0.88[EUR][1000 genomes]
rs17503792	0.93[EUR][1000 genomes]
rs17559587	0.82[GIH][hapmap];1.00[TSI][hapmap]
rs17561781	0.82[EUR][1000 genomes]
rs17562010	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17562052	0.88[EUR][1000 genomes]
rs17568665	0.88[EUR][1000 genomes]
rs17569049	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17569145	0.93[EUR][1000 genomes]
rs1870834	0.82[ASN][1000 genomes]
rs1876086	1.00[TSI][hapmap]
rs28617210	0.90[EUR][1000 genomes]
rs56793390	0.91[ASN][1000 genomes]
rs6687755	0.86[EUR][1000 genomes]
rs73125707	0.88[EUR][1000 genomes]
rs74147627	0.82[ASN][1000 genomes]
rs954615	1.00[CEU][hapmap];0.88[EUR][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	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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:225813800-225838600	Weak transcription	HMEC	breast
3	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:225816000-225838600	Weak transcription	Fetal Kidney	kidney
6	chr1:225825600-225839600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:225826200-225838800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:225826200-225839400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225830200-225838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:225830400-225838200	Weak transcription	Pancreas	Pancrea
11	chr1:225830400-225839200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:225830400-225839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:225830400-225839600	Weak transcription	Gastric	stomach
14	chr1:225831600-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:225832400-225838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:225833000-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:225833200-225838200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:225834200-225839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:225834400-225838200	Weak transcription	Left Ventricle	heart
20	chr1:225834600-225837800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:225834800-225839200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:225835000-225838200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:225835200-225837800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:225835400-225838000	Enhancers	Brain Hippocampus Middle	brain
25	chr1:225835600-225838400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:225836000-225837800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:225836200-225839200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:225836200-225840400	Active TSS	Right Atrium	heart
29	chr1:225836200-225842000	Active TSS	Aorta	Aorta
30	chr1:225836400-225837800	Enhancers	HSMMtube	muscle
31	chr1:225836600-225838200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:225836600-225841400	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:225836600-225842200	Active TSS	Right Ventricle	heart
34	chr1:225836600-225842200	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:225836800-225837800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:225836800-225837800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:225836800-225838000	Enhancers	Brain Anterior Caudate	brain
38	chr1:225836800-225838200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr1:225836800-225838800	Enhancers	Brain Substantia Nigra	brain
40	chr1:225836800-225842200	Active TSS	NHLF	lung
41	chr1:225837000-225837800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:225837000-225838200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr1:225837000-225838200	Flanking Active TSS	Fetal Brain Female	brain
44	chr1:225837000-225838200	Flanking Active TSS	HepG2	liver
45	chr1:225837000-225842000	Active TSS	Ovary	ovary
46	chr1:225837000-225842800	Active TSS	Psoas Muscle	Psoas
47	chr1:225837200-225837800	Active TSS	Fetal Stomach	stomach
48	chr1:225837200-225837800	Enhancers	NHEK	skin
49	chr1:225837200-225838400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:225837200-225839000	Weak transcription	Brain Cingulate Gyrus	brain

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