Variant report

Variant	rs11169754
Chromosome Location	chr12:51581565-51581566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51474666..51478844-chr12:51578009..51583588,6	MCF-7	breast:
2	chr12:51580860..51582633-chr17:57922811..57925538,2	MCF-7	breast:
3	chr12:51565656..51568783-chr12:51579080..51582144,3	K562	blood:
4	chr12:51581274..51584144-chr12:51584768..51587377,2	K562	blood:
5	chr12:51581106..51583160-chr12:51585274..51587538,3	K562	blood:
6	chr12:51570670..51572206-chr12:51580870..51582491,2	K562	blood:

Variant related genes	Relation type
ENSG00000135457	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1056897	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169726	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169727	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169729	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169731	0.83[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169732	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169736	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169742	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169743	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169752	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11738	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12809832	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12810455	0.84[AMR][1000 genomes]
rs12810700	0.82[AMR][1000 genomes]
rs12811508	0.86[AMR][1000 genomes]
rs12814498	0.82[AMR][1000 genomes]
rs12819225	0.86[AMR][1000 genomes]
rs12819517	0.86[AMR][1000 genomes]
rs12820559	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12829630	0.84[AMR][1000 genomes]
rs12833565	0.84[AMR][1000 genomes]
rs17296192	0.86[AMR][1000 genomes]
rs34481246	0.86[AMR][1000 genomes]
rs34498074	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6580792	0.86[AMR][1000 genomes]
rs6580793	0.84[AMR][1000 genomes]
rs67293043	0.84[AMR][1000 genomes]
rs7958064	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7964570	0.82[AMR][1000 genomes]
rs7977104	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51567400-51583400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51567400-51584000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:51567400-51610600	Weak transcription	Right Atrium	heart
4	chr12:51574800-51583400	Weak transcription	Aorta	Aorta
5	chr12:51575600-51583600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51575800-51583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:51577600-51582400	Weak transcription	Brain Substantia Nigra	brain
8	chr12:51577600-51583000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:51577800-51582000	Weak transcription	Brain Anterior Caudate	brain
10	chr12:51577800-51583400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:51578000-51582200	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:51578000-51583000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:51578000-51583400	Weak transcription	Left Ventricle	heart
14	chr12:51578000-51583400	Weak transcription	Ovary	ovary
15	chr12:51578000-51583600	Weak transcription	Pancreas	Pancrea
16	chr12:51578000-51587600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:51578200-51582200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:51578200-51582200	Weak transcription	Brain Germinal Matrix	brain
19	chr12:51578200-51586000	Weak transcription	Fetal Heart	heart
20	chr12:51578200-51596800	Weak transcription	Fetal Lung	lung
21	chr12:51578400-51583800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:51579000-51583000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:51579400-51581600	Weak transcription	Fetal Brain Female	brain
24	chr12:51579600-51583600	Enhancers	Fetal Thymus	thymus
25	chr12:51580000-51581600	Enhancers	Primary hematopoietic stem cells	blood
26	chr12:51580000-51581600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr12:51580200-51581600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr12:51580200-51581800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:51580200-51582200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:51580200-51582200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:51580200-51582200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:51580200-51582600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:51580200-51583200	Enhancers	Primary B cells from peripheral blood	blood
34	chr12:51580200-51583400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:51580200-51583400	Weak transcription	Right Ventricle	heart
36	chr12:51580400-51583400	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:51580400-51583600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:51580400-51592000	Weak transcription	Gastric	stomach
39	chr12:51580600-51581800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:51580600-51581800	Enhancers	Fetal Stomach	stomach
41	chr12:51580600-51582200	Bivalent Enhancer	HepG2	liver
42	chr12:51580600-51583400	Weak transcription	Fetal Intestine Small	intestine
43	chr12:51580600-51583800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:51580600-51587800	Weak transcription	Placenta	Placenta
45	chr12:51580600-51595800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:51580800-51581600	Enhancers	Brain Angular Gyrus	brain
47	chr12:51580800-51581600	Active TSS	Fetal Muscle Trunk	muscle
48	chr12:51580800-51582400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:51580800-51583400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:51580800-51596800	Weak transcription	Primary T cells from cord blood	blood

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