Variant report

Variant	rs11050147
Chromosome Location	chr12:29395679-29395680
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29241262..29242110-chr12:29395220..29395818,2	MCF-7	breast:
2	chr12:29394990..29395795-chr12:29470382..29471222,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257176	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1006410	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1072724	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843376	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843385	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11050149	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11050168	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12301475	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578931	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12581107	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17715086	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2288128	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288129	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2350315	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782505	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3782510	0.85[EUR][1000 genomes]
rs3948497	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4277150	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931170	0.84[AFR][1000 genomes]
rs4931171	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299283	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7313552	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7315346	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7358667	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7964831	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs986072	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11050147	RP11-996F15.2	cis	lung	GTEx
rs11050147	RP11-996F15.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29391600-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:29391800-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:29392800-29396000	Enhancers	Placenta	Placenta
4	chr12:29393200-29396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr12:29393200-29397000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:29393400-29396000	Enhancers	Duodenum Mucosa	Duodenum
7	chr12:29393400-29396600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:29394000-29395800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:29394000-29395800	Enhancers	Stomach Smooth Muscle	stomach
10	chr12:29394000-29396200	Enhancers	Colonic Mucosa	Colon
11	chr12:29394000-29396200	Enhancers	NHDF-Ad	bronchial
12	chr12:29394200-29396000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:29394200-29396200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr12:29394200-29396200	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr12:29394200-29396800	Enhancers	Stomach Mucosa	stomach
16	chr12:29394400-29395800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:29394400-29395800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:29394400-29396000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:29394400-29396200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:29394400-29396400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:29394400-29397600	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr12:29394400-29397800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:29394600-29395800	Enhancers	Brain Angular Gyrus	brain
24	chr12:29394600-29395800	Enhancers	Fetal Muscle Leg	muscle
25	chr12:29394600-29395800	Enhancers	Hela-S3	cervix
26	chr12:29394600-29395800	Enhancers	NHLF	lung
27	chr12:29394600-29396000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr12:29394600-29396200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:29394600-29396200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:29394600-29396200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:29394600-29396200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:29394600-29396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:29394600-29396200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:29394600-29396200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:29394600-29396200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:29394600-29396200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:29394600-29396200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:29394600-29396200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr12:29394600-29396200	Enhancers	HMEC	breast
40	chr12:29394600-29396200	Enhancers	NH-A	brain
41	chr12:29394600-29396400	Enhancers	Liver	Liver
42	chr12:29394600-29396600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:29394600-29396600	Enhancers	Fetal Intestine Small	intestine
44	chr12:29394600-29396600	Enhancers	Fetal Kidney	kidney
45	chr12:29394600-29396800	Enhancers	Fetal Intestine Large	intestine
46	chr12:29394600-29396800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr12:29394600-29396800	Enhancers	GM12878-XiMat	blood
48	chr12:29394800-29395800	Enhancers	Brain Cingulate Gyrus	brain
49	chr12:29394800-29395800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr12:29394800-29396200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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