Variant report

Variant	rs55684344
Chromosome Location	chr12:104356252-104356253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104355797-104356802	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:104356234-104357190	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:104356173-104356867	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:104356154-104356747	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr12:104356251-104356675	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:104356217-104356796	MCF-7	breast:	n/a	n/a
7	POLR2A	chr12:104356133-104356729	K562	blood:	n/a	n/a
8	POLR2A	chr12:104356140-104357240	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:104356239-104356757	Raji	blood:	n/a	n/a
10	POLR2A	chr12:104355625-104356841	K562	blood:	n/a	n/a
11	POLR2A	chr12:104356234-104356662	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:104356247-104356722	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:104356136-104356653	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr12:104356199-104356712	K562	blood:	n/a	n/a
15	POLR2A	chr12:104356231-104356735	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104354928..104356634-chr12:104388334..104391099,2	MCF-7	breast:
2	chr12:104324052..104326463-chr12:104355875..104358112,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDG-1	chr12:104356173-104356953	NONHSAT030400

No data

Variant related genes	Relation type
TDG	TF binding region
ENSG00000265072	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10047614	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861150	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861151	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366629	1.00[ASN][1000 genomes]
rs12369231	1.00[ASN][1000 genomes]
rs12372540	1.00[ASN][1000 genomes]
rs17805003	1.00[ASN][1000 genomes]
rs1866074	1.00[ASN][1000 genomes]
rs4135044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135045	0.81[AFR][1000 genomes]
rs4135063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135093	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56219801	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369424	1.00[ASN][1000 genomes]
rs6539116	1.00[ASN][1000 genomes]
rs7136550	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138850	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306515	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313381	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1799879	chr12:104351057-104360713	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104351400-104358000	Weak transcription	Lung	lung
2	chr12:104351400-104358000	Weak transcription	Spleen	Spleen
3	chr12:104351600-104356400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:104351600-104356400	Weak transcription	Brain Angular Gyrus	brain
5	chr12:104351600-104357000	Weak transcription	Fetal Brain Female	brain
6	chr12:104351600-104357200	Weak transcription	GM12878-XiMat	blood
7	chr12:104351600-104357400	Weak transcription	Fetal Lung	lung
8	chr12:104351600-104357400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:104351600-104357600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:104351600-104357600	Weak transcription	NHLF	lung
11	chr12:104351600-104357800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:104351600-104357800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:104351600-104357800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:104351600-104357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:104351600-104357800	Weak transcription	HSMMtube	muscle
16	chr12:104351600-104357800	Weak transcription	NHDF-Ad	bronchial
17	chr12:104351600-104357800	Weak transcription	NHEK	skin
18	chr12:104351600-104357800	Weak transcription	Osteobl	bone
19	chr12:104351600-104358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:104351600-104358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:104351600-104358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:104351600-104358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:104351600-104358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:104351600-104358000	Weak transcription	Esophagus	oesophagus
25	chr12:104351600-104358000	Weak transcription	Fetal Intestine Small	intestine
26	chr12:104351600-104358000	Weak transcription	Ovary	ovary
27	chr12:104351600-104358000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:104351600-104358000	Weak transcription	Right Ventricle	heart
29	chr12:104351600-104358000	Weak transcription	Thymus	Thymus
30	chr12:104351600-104358000	Weak transcription	HMEC	breast
31	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
38	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
39	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
41	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:104352000-104357600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:104352000-104357600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:104352000-104357800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr12:104352000-104357800	Weak transcription	Adipose Nuclei	Adipose
48	chr12:104352000-104357800	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:104352000-104358000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:104352000-104358000	Weak transcription	Left Ventricle	heart

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