Variant report

Variant	rs12824716
Chromosome Location	chr12:46867911-46867912
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46763709..46766577-chr12:46865824..46870117,4	K562	blood:
2	chr12:46867765..46869816-chr12:46873759..46876324,2	K562	blood:
3	chr12:46857526..46859603-chr12:46866422..46869181,2	MCF-7	breast:
4	chr12:46775882..46782891-chr12:46867252..46874732,11	MCF-7	breast:
5	chr12:46848032..46851885-chr12:46865278..46868911,4	MCF-7	breast:
6	chr12:46853187..46855713-chr12:46867709..46870623,2	K562	blood:
7	chr12:46865786..46868659-chr12:46883028..46885506,2	MCF-7	breast:
8	chr12:46764487..46767688-chr12:46865633..46870599,8	MCF-7	breast:
9	chr12:46865908..46869326-chr12:46872874..46876694,4	MCF-7	breast:
10	chr12:46750575..46752943-chr12:46867557..46871198,3	K562	blood:
11	chr12:46867596..46869336-chr12:46885001..46888174,3	MCF-7	breast:

No data

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

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11183468	0.82[CHB][hapmap]
rs4073925	0.81[AMR][1000 genomes]
rs4076248	0.82[CHB][hapmap]
rs4768697	1.00[ASW][hapmap];0.82[MEX][hapmap]
rs7965930	1.00[YRI][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12824716	LOC100288798	cis	hippocampus	BrainEAC

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:46856200-46868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:46864000-46868600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:46864200-46877400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:46864400-46877400	Weak transcription	Primary T cells from cord blood	blood
6	chr12:46864800-46868600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:46864800-46868600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:46864800-46868600	Enhancers	Stomach Mucosa	stomach
9	chr12:46864800-46868600	Enhancers	HMEC	breast
10	chr12:46864800-46868800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:46865000-46868200	Weak transcription	Spleen	Spleen
12	chr12:46865400-46870200	Weak transcription	Lung	lung
13	chr12:46865400-46879200	Weak transcription	Right Ventricle	heart
14	chr12:46865600-46868800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:46865800-46868000	Enhancers	Fetal Heart	heart
16	chr12:46866000-46868400	Enhancers	Fetal Intestine Large	intestine
17	chr12:46866000-46868800	Enhancers	Colon Smooth Muscle	Colon
18	chr12:46866000-46868800	Enhancers	Fetal Kidney	kidney
19	chr12:46866200-46868600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:46866200-46868600	Enhancers	Fetal Intestine Small	intestine
21	chr12:46866200-46868600	Enhancers	Fetal Stomach	stomach
22	chr12:46866200-46868800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr12:46866400-46868000	Weak transcription	Ovary	ovary
24	chr12:46866400-46868000	Weak transcription	Right Atrium	heart
25	chr12:46866400-46868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:46866400-46868200	Weak transcription	Left Ventricle	heart
27	chr12:46866400-46871000	Weak transcription	Gastric	stomach
28	chr12:46866400-46871400	Weak transcription	Dnd41	blood
29	chr12:46866600-46868000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:46866600-46868000	Weak transcription	Pancreas	Pancrea
31	chr12:46866800-46868200	Flanking Active TSS	HUVEC	blood vessel
32	chr12:46867000-46868000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:46867000-46868000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr12:46867000-46868000	Active TSS	A549	lung
35	chr12:46867000-46868200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:46867200-46868000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:46867200-46868000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:46867200-46868000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:46867200-46868200	Enhancers	Primary B cells from peripheral blood	blood
40	chr12:46867200-46868200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:46867200-46868200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:46867400-46868000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:46867400-46868000	Enhancers	Psoas Muscle	Psoas
44	chr12:46867400-46868000	Flanking Active TSS	Hela-S3	cervix
45	chr12:46867400-46868000	Flanking Active TSS	HSMMtube	muscle
46	chr12:46867400-46868000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr12:46867400-46868000	Flanking Active TSS	NH-A	brain
48	chr12:46867400-46868000	Flanking Active TSS	NHEK	skin
49	chr12:46867400-46868200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:46867400-46868200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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