Variant report

Variant	rs57489906
Chromosome Location	chr12:49967042-49967043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49747941..49749932-chr12:49965800..49968096,2	MCF-7	breast:
2	chr12:49965859..49967521-chr12:49975091..49977104,2	MCF-7	breast:
3	chr12:49959993..49964620-chr12:49965374..49976382,20	MCF-7	breast:
4	chr12:49964375..49969334-chr12:49981796..49986330,5	MCF-7	breast:
5	chr12:49658087..49660449-chr12:49965651..49968342,2	K562	blood:
6	chr12:49965875..49968503-chr12:49968843..49972446,3	MCF-7	breast:
7	chr12:49955950..49959693-chr12:49966326..49968627,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110844	Chromatin interaction
ENSG00000257964	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11830472	0.90[AFR][1000 genomes]
rs11831670	0.90[AFR][1000 genomes]
rs11831673	0.90[AFR][1000 genomes]
rs11831877	0.81[AFR][1000 genomes]
rs11832420	0.96[AFR][1000 genomes]
rs11832727	0.81[AFR][1000 genomes]
rs11833472	0.96[AFR][1000 genomes]
rs11834570	0.81[AFR][1000 genomes]
rs11835085	0.90[AFR][1000 genomes]
rs11837399	0.81[AFR][1000 genomes]
rs11837408	0.81[AFR][1000 genomes]
rs3861577	1.00[AFR][1000 genomes]
rs56840810	0.93[AFR][1000 genomes]
rs57905415	0.81[AFR][1000 genomes]
rs59597892	0.81[AFR][1000 genomes]
rs59628479	0.81[AFR][1000 genomes]
rs60117004	0.81[AFR][1000 genomes]
rs7131756	0.81[AFR][1000 genomes]
rs7134329	0.81[AFR][1000 genomes]
rs7307183	0.81[AFR][1000 genomes]
rs7310069	1.00[AFR][1000 genomes]
rs7312037	0.81[AFR][1000 genomes]
rs7313183	0.81[AFR][1000 genomes]
rs7313590	0.81[AFR][1000 genomes]
rs7960185	0.93[AFR][1000 genomes]
rs7973011	0.90[AFR][1000 genomes]
rs7978381	0.90[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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49962600-49970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:49962600-49971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:49962800-49970800	Weak transcription	Lung	lung
4	chr12:49962800-49974200	Weak transcription	Esophagus	oesophagus
5	chr12:49962800-49974200	Weak transcription	Placenta	Placenta
6	chr12:49963000-49967600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:49963000-49967800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:49963000-49968600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:49963000-49969600	Weak transcription	NH-A	brain
10	chr12:49963000-49970600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:49963000-49971600	Weak transcription	Right Atrium	heart
12	chr12:49963000-49974000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:49963000-49974000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:49963000-49974000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:49963000-49974000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:49963000-49974000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:49963000-49974000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:49963000-49974000	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:49963000-49974000	Weak transcription	Brain Substantia Nigra	brain
20	chr12:49963000-49974000	Weak transcription	HSMMtube	muscle
21	chr12:49963000-49974200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:49963000-49974200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:49963000-49974200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:49963000-49974200	Weak transcription	Fetal Kidney	kidney
25	chr12:49963000-49974200	Weak transcription	Fetal Lung	lung
26	chr12:49963000-49974200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:49963000-49979200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:49963000-49979200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:49963000-49982200	Weak transcription	NHLF	lung
30	chr12:49963000-49984800	Weak transcription	Small Intestine	intestine
31	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
32	chr12:49963200-49967200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:49963200-49967200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:49963200-49967200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:49963200-49967400	Weak transcription	Liver	Liver
36	chr12:49963200-49967800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:49963200-49967800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:49963200-49967800	Weak transcription	Primary T cells from cord blood	blood
39	chr12:49963200-49968600	Weak transcription	Fetal Intestine Small	intestine
40	chr12:49963200-49969800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:49963200-49971400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:49963200-49971400	Weak transcription	Left Ventricle	heart
43	chr12:49963200-49972200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:49963200-49974000	Weak transcription	Brain Anterior Caudate	brain
45	chr12:49963200-49974000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:49963200-49974000	Weak transcription	A549	lung
47	chr12:49963200-49974000	Weak transcription	HSMM	muscle
48	chr12:49963200-49974200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:49963200-49974200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:49963200-49974200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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