Variant report

Variant	rs12139824
Chromosome Location	chr1:225815038-225815039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225812132..225816261-chr1:225840645..225843021,5	MCF-7	breast:
2	chr1:225812743..225815583-chr1:225838779..225842082,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12120530	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12408092	0.87[EUR][1000 genomes]
rs34718899	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41304129	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72753023	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs72753057	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
4	chr1:225797200-225815200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:225806200-225817600	Weak transcription	Fetal Brain Female	brain
6	chr1:225806400-225815200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:225807200-225820400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:225808200-225818400	Weak transcription	Fetal Brain Male	brain
9	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:225810000-225825400	Weak transcription	NHEK	skin
11	chr1:225810600-225815200	Weak transcription	Pancreas	Pancrea
12	chr1:225810600-225815600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:225812400-225815800	Enhancers	Fetal Lung	lung
14	chr1:225812400-225816000	Enhancers	Ovary	ovary
15	chr1:225812400-225816000	Enhancers	Stomach Smooth Muscle	stomach
16	chr1:225812600-225816200	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr1:225812600-225816200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:225812600-225816400	Enhancers	Colon Smooth Muscle	Colon
19	chr1:225812800-225824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:225812800-225825000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:225813000-225815200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:225813000-225815400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:225813200-225815800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:225813200-225816000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:225813200-225816400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:225813200-225816400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:225813200-225816400	Enhancers	Rectal Smooth Muscle	rectum
28	chr1:225813400-225824800	Weak transcription	Lung	lung
29	chr1:225813600-225815400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:225813600-225815800	Enhancers	Brain Substantia Nigra	brain
31	chr1:225813600-225816000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:225813600-225837600	Weak transcription	HUVEC	blood vessel
33	chr1:225813800-225815200	Enhancers	Right Ventricle	heart
34	chr1:225813800-225815400	Enhancers	NH-A	brain
35	chr1:225813800-225815600	Enhancers	NHLF	lung
36	chr1:225813800-225815800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:225813800-225815800	Enhancers	Left Ventricle	heart
38	chr1:225813800-225815800	Enhancers	Stomach Mucosa	stomach
39	chr1:225813800-225816000	Enhancers	Fetal Intestine Small	intestine
40	chr1:225813800-225816000	Enhancers	Fetal Muscle Leg	muscle
41	chr1:225813800-225816200	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:225813800-225816200	Enhancers	Brain Hippocampus Middle	brain
43	chr1:225813800-225817200	Enhancers	Psoas Muscle	Psoas
44	chr1:225813800-225838600	Weak transcription	HMEC	breast
45	chr1:225814000-225815600	Enhancers	NHDF-Ad	bronchial
46	chr1:225814000-225815800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:225814000-225815800	Enhancers	Fetal Intestine Large	intestine
48	chr1:225814000-225816000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:225814000-225816200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:225814000-225816800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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