Variant report

Variant	rs55780086
Chromosome Location	chr12:104358127-104358128
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104357713-104358480	K562	blood:	n/a	n/a
2	POLR2A	chr12:104358049-104358547	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:104358052-104360401	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:104357794-104360395	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:104358120-104358594	K562	blood:	n/a	n/a
6	POLR2A	chr12:104357948-104358415	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:104357812-104358281	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:104358119-104358253	ProgFib	skin:	n/a	n/a
9	POLR2A	chr12:104358049-104358863	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:104358049..104359986-chr12:104530882..104532737,3	K562	blood:
2	chr12:104356512..104358461-chr12:104416021..104418355,2	K562	blood:
3	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:
4	chr12:104357292..104359018-chr12:104494120..104496296,2	MCF-7	breast:
5	chr12:104357850..104359549-chr12:104531019..104533949,2	K562	blood:
6	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
7	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
8	chr12:104328917..104332179-chr12:104357230..104361045,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf73-2	chr12:104357568-104359481	NONHSAT030401

No data

Variant related genes	Relation type
TDG	TF binding region
ENSG00000120837	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000265072	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10778307	0.88[EUR][1000 genomes]
rs11111864	0.87[EUR][1000 genomes]
rs12426183	1.00[AFR][1000 genomes]
rs12426202	1.00[AFR][1000 genomes]
rs12426220	1.00[AFR][1000 genomes]
rs12426382	0.94[EUR][1000 genomes]
rs17034946	0.94[EUR][1000 genomes]
rs17034960	0.94[EUR][1000 genomes]
rs17180749	1.00[AFR][1000 genomes]
rs17795280	1.00[AFR][1000 genomes]
rs1882019	0.97[EUR][1000 genomes]
rs2293626	0.87[EUR][1000 genomes]
rs2888805	0.95[EUR][1000 genomes]
rs35193500	1.00[AFR][1000 genomes]
rs3751207	1.00[EUR][1000 genomes]
rs3751208	1.00[EUR][1000 genomes]
rs3829300	1.00[EUR][1000 genomes]
rs4135060	0.90[EUR][1000 genomes]
rs4135065	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135076	1.00[EUR][1000 genomes]
rs4135078	1.00[EUR][1000 genomes]
rs4135082	1.00[EUR][1000 genomes]
rs4135085	1.00[EUR][1000 genomes]
rs4135086	1.00[EUR][1000 genomes]
rs4135087	1.00[EUR][1000 genomes]
rs4135094	1.00[EUR][1000 genomes]
rs4135095	1.00[EUR][1000 genomes]
rs4135118	0.95[EUR][1000 genomes]
rs4135131	0.95[EUR][1000 genomes]
rs4135150	0.89[EUR][1000 genomes]
rs55893407	0.85[EUR][1000 genomes]
rs60534873	1.00[EUR][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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
8	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
9	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
11	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:104352000-104358400	Weak transcription	Primary B cells from cord blood	blood
15	chr12:104352200-104358200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:104353000-104358200	Weak transcription	Hela-S3	cervix
17	chr12:104356600-104358200	Enhancers	HepG2	liver
18	chr12:104357000-104358400	Enhancers	Brain Angular Gyrus	brain
19	chr12:104357200-104358200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:104357200-104358200	Weak transcription	Fetal Brain Female	brain
21	chr12:104357400-104358200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:104357400-104358400	Enhancers	Fetal Lung	lung
23	chr12:104357600-104358200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:104357600-104358200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:104357600-104358200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr12:104357600-104358200	Enhancers	Fetal Heart	heart
27	chr12:104357600-104358200	Enhancers	A549	lung
28	chr12:104357600-104358600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:104357600-104358600	Enhancers	Primary hematopoietic stem cells	blood
30	chr12:104357600-104358600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr12:104357600-104359000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:104357800-104358200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:104357800-104358200	Enhancers	Adipose Nuclei	Adipose
34	chr12:104357800-104358200	Enhancers	Duodenum Mucosa	Duodenum
35	chr12:104357800-104358200	Enhancers	Fetal Muscle Leg	muscle
36	chr12:104357800-104358200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:104357800-104358200	Enhancers	Dnd41	blood
38	chr12:104357800-104358200	Enhancers	HSMM	muscle
39	chr12:104357800-104358200	Enhancers	NH-A	brain
40	chr12:104357800-104358200	Enhancers	NHEK	skin
41	chr12:104357800-104358400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:104357800-104358400	Enhancers	Colon Smooth Muscle	Colon
43	chr12:104357800-104358400	Enhancers	Fetal Brain Male	brain
44	chr12:104357800-104358400	Enhancers	Fetal Kidney	kidney
45	chr12:104357800-104358400	Enhancers	Psoas Muscle	Psoas
46	chr12:104357800-104358400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr12:104357800-104358600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr12:104357800-104358600	Flanking Active TSS	K562	blood
49	chr12:104357800-104358800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr12:104357800-104358800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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