Variant report

Variant	rs12827740
Chromosome Location	chr12:46848115-46848116
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46844018..46846962-chr12:46848048..46851671,5	MCF-7	breast:
2	chr12:46760174..46765075-chr12:46847808..46852227,4	MCF-7	breast:
3	chr12:46764073..46768493-chr12:46846850..46851385,16	MCF-7	breast:
4	chr12:46848032..46851885-chr12:46865278..46868911,4	MCF-7	breast:
5	chr12:46835571..46842966-chr12:46847412..46853177,10	MCF-7	breast:
6	chr12:46751021..46753998-chr12:46846129..46848117,2	K562	blood:
7	chr12:46764096..46767678-chr12:46847759..46851416,3	K562	blood:
8	chr12:46765219..46768267-chr12:46847099..46854235,10	MCF-7	breast:
9	chr12:46775191..46782074-chr12:46843960..46851522,20	MCF-7	breast:
10	chr12:46826312..46828736-chr12:46847839..46850473,2	MCF-7	breast:
11	chr12:46840761..46844133-chr12:46846897..46850857,3	K562	blood:
12	chr12:46847999..46849611-chr12:46871552..46873067,2	MCF-7	breast:
13	chr12:46662134..46664128-chr12:46848113..46849835,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000257496	Chromatin interaction
ENSG00000258096	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000257261	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10748450	0.93[AMR][1000 genomes]
rs10785628	0.90[AMR][1000 genomes]
rs10785629	0.93[AMR][1000 genomes]
rs10880973	0.93[AMR][1000 genomes]
rs10880974	0.83[AMR][1000 genomes]
rs11183502	0.82[AMR][1000 genomes]
rs11183503	0.82[AMR][1000 genomes]
rs11183504	0.82[AMR][1000 genomes]
rs11837427	0.82[AMR][1000 genomes]
rs12313929	0.83[AMR][1000 genomes]
rs12813763	0.82[EUR][1000 genomes]
rs12814298	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12814341	0.82[EUR][1000 genomes]
rs12832425	0.82[EUR][1000 genomes]
rs3925101	0.83[AMR][1000 genomes]
rs4077707	0.89[AMR][1000 genomes]
rs4077708	0.90[AMR][1000 genomes]
rs4768121	0.82[EUR][1000 genomes]
rs4768123	0.90[AMR][1000 genomes]
rs4768723	0.90[AMR][1000 genomes]
rs4768724	0.93[AMR][1000 genomes]
rs4768725	0.93[AMR][1000 genomes]
rs4768726	0.82[AMR][1000 genomes]
rs4768727	0.83[AMR][1000 genomes]
rs4768728	0.82[AMR][1000 genomes]
rs4768729	0.82[AMR][1000 genomes]
rs4768730	0.83[AMR][1000 genomes]
rs6582657	0.93[AMR][1000 genomes]
rs6582658	0.93[AMR][1000 genomes]
rs6582660	0.83[AMR][1000 genomes]
rs6582661	0.83[AMR][1000 genomes]
rs6582663	0.83[AMR][1000 genomes]
rs7301001	0.82[EUR][1000 genomes]
rs7486915	0.83[AMR][1000 genomes]
rs7488144	0.83[AMR][1000 genomes]
rs7488577	0.82[AMR][1000 genomes]
rs7954645	0.83[AMR][1000 genomes]
rs7956314	0.83[AMR][1000 genomes]
rs7960808	0.83[AMR][1000 genomes]
rs7964767	0.83[AMR][1000 genomes]
rs7980455	0.82[AMR][1000 genomes]
rs9706162	0.82[AMR][1000 genomes]
rs9706460	0.82[AMR][1000 genomes]
rs9706520	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46821600-46848600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:46828000-46856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:46843200-46850600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:46843800-46850400	Enhancers	HMEC	breast
5	chr12:46843800-46850800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:46844200-46849600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:46844400-46848600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:46844400-46848600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:46844400-46848600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:46844400-46848600	Weak transcription	Placenta	Placenta
11	chr12:46844400-46848600	Weak transcription	Gastric	stomach
12	chr12:46844400-46849600	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:46844400-46849800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:46844400-46849800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:46844400-46853200	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:46844600-46848400	Weak transcription	Dnd41	blood
17	chr12:46844600-46848600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:46844600-46848600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:46844600-46848600	Weak transcription	Fetal Thymus	thymus
20	chr12:46844600-46848800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:46844600-46849600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:46844600-46849600	Weak transcription	Fetal Lung	lung
23	chr12:46844600-46849800	Weak transcription	Adipose Nuclei	Adipose
24	chr12:46844600-46849800	Weak transcription	Fetal Stomach	stomach
25	chr12:46844600-46849800	Weak transcription	NH-A	brain
26	chr12:46844600-46849800	Weak transcription	Osteobl	bone
27	chr12:46844600-46851800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:46844600-46852000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:46844600-46852200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:46844600-46852400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:46844600-46853000	Weak transcription	Brain Substantia Nigra	brain
32	chr12:46844600-46853200	Weak transcription	Left Ventricle	heart
33	chr12:46844600-46854000	Weak transcription	Fetal Intestine Small	intestine
34	chr12:46844600-46854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:46844600-46854800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:46844600-46855200	Weak transcription	Right Ventricle	heart
37	chr12:46844600-46866000	Weak transcription	Fetal Intestine Large	intestine
38	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:46844800-46848400	Weak transcription	Primary T cells from cord blood	blood
40	chr12:46844800-46848400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:46844800-46848600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr12:46844800-46848600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:46844800-46848600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:46844800-46848600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:46844800-46848800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:46844800-46849800	Weak transcription	Right Atrium	heart
47	chr12:46844800-46853000	Weak transcription	Spleen	Spleen
48	chr12:46844800-46855200	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:46845000-46848400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr12:46845200-46848800	Weak transcription	Monocytes-CD14+_RO01746	blood

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