Variant report

Variant	rs58992779
Chromosome Location	chr12:45655740-45655741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45649985..45652143-chr12:45652461..45655864,3	MCF-7	breast:
2	chr12:45654235..45656718-chr12:45666957..45669692,2	MCF-7	breast:
3	chr12:45654342..45656870-chr12:45658694..45660838,2	MCF-7	breast:
4	chr12:45608273..45611402-chr12:45650771..45657484,8	MCF-7	breast:
5	chr12:45655142..45658052-chr12:45658399..45661222,2	MCF-7	breast:
6	chr12:45653667..45656003-chr12:46121465..46123102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177119	Chromatin interaction
ENSG00000134297	Chromatin interaction
ENSG00000273015	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs17095452	0.91[AFR][1000 genomes]
rs55994528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56162044	1.00[AMR][1000 genomes]
rs56409009	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56672176	0.90[AFR][1000 genomes]
rs56842412	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57283482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57514011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57516582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57590365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57752448	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58025806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58379974	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58615264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58938625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59111701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59344692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59579391	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60098273	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60717004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61226604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61679354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61740396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080326	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080682	0.90[AFR][1000 genomes]
rs74080804	1.00[AMR][1000 genomes]
rs74080853	0.90[AFR][1000 genomes]
rs74080929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083303	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083306	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083403	0.86[AFR][1000 genomes]
rs74083404	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083405	0.87[AFR][1000 genomes];1.00[AMR][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	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45636200-45662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:45648000-45657400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:45651200-45662000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:45651400-45662000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:45651400-45662400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:45651400-45675600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:45651600-45656600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:45651600-45656600	Weak transcription	GM12878-XiMat	blood
9	chr12:45651600-45657200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:45651600-45662000	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:45651600-45662400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:45651600-45667000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:45651600-45667400	Weak transcription	Brain Substantia Nigra	brain
14	chr12:45651600-45674000	Weak transcription	Primary B cells from cord blood	blood
15	chr12:45653800-45657400	Weak transcription	Small Intestine	intestine
16	chr12:45653800-45662000	Weak transcription	Esophagus	oesophagus
17	chr12:45654200-45655800	Enhancers	Adipose Nuclei	Adipose
18	chr12:45654200-45656600	Weak transcription	Fetal Heart	heart
19	chr12:45654200-45657800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:45654200-45662000	Weak transcription	Right Ventricle	heart
21	chr12:45654200-45662000	Weak transcription	Spleen	Spleen
22	chr12:45654200-45662400	Weak transcription	Gastric	stomach
23	chr12:45654200-45666800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:45654400-45655800	Enhancers	Liver	Liver
25	chr12:45654400-45655800	Enhancers	HepG2	liver
26	chr12:45654400-45656000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:45654400-45656400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:45654400-45656600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:45654400-45656600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:45654400-45657000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:45654400-45657200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:45654400-45657200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:45654400-45657200	Weak transcription	Right Atrium	heart
34	chr12:45654400-45657200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:45654400-45657200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:45654400-45657200	Weak transcription	K562	blood
37	chr12:45654400-45657400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:45654400-45657400	Weak transcription	Fetal Kidney	kidney
39	chr12:45654400-45661800	Weak transcription	A549	lung
40	chr12:45654400-45662000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:45654400-45662000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:45654400-45662000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:45654400-45662000	Weak transcription	Osteobl	bone
44	chr12:45654400-45662400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:45654400-45662400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:45654400-45662400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:45654400-45662400	Weak transcription	Fetal Stomach	stomach
48	chr12:45654400-45662400	Weak transcription	HSMM	muscle
49	chr12:45654400-45662400	Weak transcription	NH-A	brain
50	chr12:45654400-45662400	Weak transcription	NHLF	lung

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