Variant report

Variant	rs11715146
Chromosome Location	chr3:113001462-113001463
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112994340..112996390-chr3:112999455..113002856,3	MCF-7	breast:
2	chr3:112359608..112361417-chr3:113001269..113003641,2	MCF-7	breast:
3	chr3:113000767..113002903-chr3:113003436..113005899,2	MCF-7	breast:
4	chr3:112998546..113000048-chr3:113000099..113002226,2	MCF-7	breast:
5	chr3:112988806..112991675-chr3:113000580..113002135,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11919134	0.81[AMR][1000 genomes]
rs16860792	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2649878	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3846046	0.80[AMR][1000 genomes]
rs3856718	0.80[AMR][1000 genomes]
rs41271357	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4682477	0.91[EUR][1000 genomes]
rs61579027	0.81[EUR][1000 genomes]
rs61586075	0.91[EUR][1000 genomes]
rs7620307	0.91[EUR][1000 genomes]
rs775219	0.91[EUR][1000 genomes]
rs775230	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288981	0.91[EUR][1000 genomes]
rs9874603	0.91[EUR][1000 genomes]
rs999366	0.91[EUR][1000 genomes]
rs999367	0.91[EUR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11715146	BOC	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
3	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:112990600-113004000	Weak transcription	NHEK	skin
5	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
7	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
12	chr3:112995400-113035800	Weak transcription	Lung	lung
13	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:112995800-113004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:112995800-113006600	Weak transcription	Fetal Brain Male	brain
17	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
19	chr3:112996000-113005800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
21	chr3:112996200-113002000	Weak transcription	NH-A	brain
22	chr3:112996200-113003000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:112996200-113004400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:112996200-113005800	Weak transcription	Osteobl	bone
25	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:112996400-113003600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:112996400-113004600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:112996600-113004200	Strong transcription	Colon Smooth Muscle	Colon
30	chr3:112996800-113002000	Strong transcription	Fetal Intestine Large	intestine
31	chr3:112996800-113003200	Strong transcription	Esophagus	oesophagus
32	chr3:112996800-113004200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:112997000-113003000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:112997000-113003200	Strong transcription	Fetal Brain Female	brain
35	chr3:112997000-113003400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:112997000-113004000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:112997000-113004000	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:112997000-113005200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:112997000-113006200	Strong transcription	Fetal Intestine Small	intestine
40	chr3:112997200-113003600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:112997200-113005400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
43	chr3:112997400-113003800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:112997400-113004000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:112997400-113004400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:112997400-113006200	Strong transcription	Fetal Stomach	stomach
47	chr3:112997600-113004600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:112997800-113005200	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:112998000-113002600	Weak transcription	Colonic Mucosa	Colon
50	chr3:112998200-113005000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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