Variant report

Variant	rs12910141
Chromosome Location	chr15:50651792-50651793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50643981-50656245	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:50651119-50651821	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50650545..50654228-chr15:50976566..50979826,3	MCF-7	breast:
2	chr1:119682098..119684548-chr15:50651200..50654157,2	MCF-7	breast:
3	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
4	chr15:50521669..50523479-chr15:50650112..50652205,2	MCF-7	breast:
5	chr15:50649363..50652046-chr15:51189573..51192655,3	MCF-7	breast:
6	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
7	chr15:50649633..50652207-chr15:51200859..51202821,2	K562	blood:
8	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABPB1-1	chr15:50651647-50651929	ENSG00000259715.1

No data

Variant related genes	Relation type
MIR4712	TF binding region
GABPB1	TF binding region
ENSG00000116874	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000231365	Chromatin interaction
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1134906	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631966	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639115	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12595107	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916674	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078139	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414047	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34943451	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774560	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4775878	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493438	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7163201	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7496811	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8027243	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8035590	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036041	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs934638	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9673053	0.86[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50648200-50653800	Weak transcription	Pancreas	Pancrea
3	chr15:50648200-50657200	Weak transcription	Esophagus	oesophagus
4	chr15:50648200-50658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:50648200-50664400	Weak transcription	Lung	lung
6	chr15:50648400-50652800	Weak transcription	Ovary	ovary
7	chr15:50648400-50660400	Weak transcription	Aorta	Aorta
8	chr15:50648800-50655600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:50649000-50653400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:50649000-50658600	Weak transcription	Right Atrium	heart
11	chr15:50649200-50652400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:50649200-50656400	Strong transcription	Fetal Muscle Leg	muscle
13	chr15:50649200-50664400	Weak transcription	Right Ventricle	heart
14	chr15:50649400-50652000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:50649400-50652400	Weak transcription	Brain Angular Gyrus	brain
16	chr15:50649400-50652600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:50649400-50653200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:50649400-50653800	Weak transcription	Brain Anterior Caudate	brain
19	chr15:50649400-50653800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:50649400-50653800	Weak transcription	Fetal Brain Female	brain
21	chr15:50649400-50653800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:50649400-50654800	Weak transcription	Brain Germinal Matrix	brain
23	chr15:50649400-50655800	Strong transcription	HSMM	muscle
24	chr15:50649400-50656600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:50649400-50657800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:50649400-50659200	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:50649400-50664000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:50649600-50652200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:50649600-50652200	Weak transcription	HMEC	breast
30	chr15:50649600-50652400	Weak transcription	Adipose Nuclei	Adipose
31	chr15:50649600-50652400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:50649600-50652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:50649600-50653000	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr15:50649600-50654000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:50649600-50654600	Strong transcription	Osteobl	bone
36	chr15:50649600-50654800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr15:50649600-50654800	Weak transcription	Brain Substantia Nigra	brain
38	chr15:50649600-50655600	Weak transcription	Gastric	stomach
39	chr15:50649600-50656600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:50649600-50656800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:50649600-50657400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:50649600-50660600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:50649600-50661800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:50649800-50652200	Weak transcription	Liver	Liver
45	chr15:50649800-50652400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:50649800-50652800	Weak transcription	Fetal Stomach	stomach
47	chr15:50649800-50653600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:50649800-50653600	Strong transcription	Brain Hippocampus Middle	brain
49	chr15:50649800-50654600	Strong transcription	Fetal Lung	lung
50	chr15:50649800-50655600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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