Variant report

Variant	rs73346380
Chromosome Location	chr12:58330632-58330633
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58330309-58330697	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:58329155-58330889	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:58329580-58330728	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA1	chr12:58329261-58330758	PBDE	blood:	n/a	chr12:58329696-58329705
5	POLR2A	chr12:58329663-58330691	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:58329433-58330739	K562	blood:	n/a	n/a
7	POLR2A	chr12:58328701-58331022	GM12891	blood:	n/a	n/a
8	MTA3	chr12:58329538-58330752	GM12878	blood:	n/a	n/a
9	ZNF274	chr12:58330263-58331012	K562	blood:	n/a	n/a
10	POLR2A	chr12:58328536-58330720	K562	blood:	n/a	n/a
11	POLR2A	chr12:58328611-58330747	K562	blood:	n/a	n/a
12	POLR2A	chr12:58329454-58330640	U87	brain:	n/a	n/a
13	IRF1	chr12:58328806-58330914	K562	blood:	n/a	chr12:58330860-58330873
14	POLR2A	chr12:58329620-58330643	GM12878	blood:	n/a	n/a
15	HCFC1	chr12:58329176-58330988	Hela-S3	cervix:	n/a	n/a
16	MXI1	chr12:58329025-58330799	SK-N-SH	brain:	n/a	chr12:58329896-58329911 chr12:58329898-58329913
17	POLR2A	chr12:58329448-58330687	U87	brain:	n/a	n/a
18	POLR2A	chr12:58329616-58330711	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:58329582-58330704	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:58328011-58330782	K562	blood:	n/a	n/a
21	JUND	chr12:58329224-58330659	K562	blood:	n/a	chr12:58329697-58329707 chr12:58329697-58329707 chr12:58329697-58329707
22	POLR2A	chr12:58330339-58330847	K562	blood:	n/a	n/a
23	POLR2A	chr12:58328674-58330767	NB4	blood:	n/a	n/a
24	POLR2A	chr12:58328501-58330747	HL-60	blood:	n/a	n/a
25	ZC3H11A	chr12:58329820-58330663	K562	blood:	n/a	n/a
26	POLR2A	chr12:58329561-58330640	GM12892	blood:	n/a	n/a
27	POLR2A	chr12:58328672-58330754	K562	blood:	n/a	n/a
28	POLR2A	chr12:58329619-58330679	GM18505	blood:	n/a	n/a
29	POLR2A	chr12:58328298-58330708	PBDE	blood:	n/a	n/a
30	MAFF	chr12:58329618-58330754	K562	blood:	n/a	n/a
31	EP300	chr12:58328672-58330669	K562	blood:	n/a	chr12:58329978-58329994 chr12:58329736-58329752 chr12:58330002-58330009 chr12:58329974-58329981
32	RCOR1	chr12:58330502-58330632	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58003448..58005159-chr12:58329612..58331307,2	K562	blood:
2	chr12:58146721..58149123-chr12:58330314..58332676,2	K562	blood:
3	chr12:58164032..58167803-chr12:58328284..58330655,5	K562	blood:
4	chr12:58238134..58241883-chr12:58327269..58331955,5	K562	blood:
5	chr12:58236777..58241883-chr12:58327592..58331955,7	K562	blood:
6	chr12:58158495..58161066-chr12:58329095..58330993,2	K562	blood:

Variant related genes	Relation type
ENSG00000257698	TF binding region
XRCC6BP1	TF binding region
ENSG00000175215	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000123427	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12304123	1.00[ASN][1000 genomes]
rs28704571	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3211627	1.00[ASN][1000 genomes]
rs4760331	1.00[AMR][1000 genomes]
rs4760336	1.00[ASN][1000 genomes]
rs56218802	1.00[AMR][1000 genomes]
rs73335533	0.81[AFR][1000 genomes]
rs73338256	1.00[AMR][1000 genomes]
rs73340215	1.00[AMR][1000 genomes]
rs73340232	1.00[AMR][1000 genomes]
rs73340240	1.00[AMR][1000 genomes]
rs73340266	1.00[AMR][1000 genomes]
rs73340267	1.00[AMR][1000 genomes]
rs73342234	1.00[AMR][1000 genomes]
rs73344379	1.00[AMR][1000 genomes]
rs73344382	1.00[AMR][1000 genomes]
rs73344386	1.00[AMR][1000 genomes]
rs73344388	1.00[AMR][1000 genomes]
rs73344397	1.00[ASN][1000 genomes]
rs73348214	1.00[AMR][1000 genomes]
rs73348217	1.00[AMR][1000 genomes]
rs7956170	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8176350	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58328800-58330800	Active TSS	K562	blood
2	chr12:58329400-58330800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:58329400-58330800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:58329400-58330800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:58329600-58330800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:58330200-58330800	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:58330200-58330800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:58330200-58330800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:58330200-58330800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:58330200-58330800	Flanking Active TSS	Dnd41	blood
11	chr12:58330200-58330800	Flanking Active TSS	Hela-S3	cervix
12	chr12:58330200-58334400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:58330200-58334400	Weak transcription	Colonic Mucosa	Colon
14	chr12:58330200-58334400	Weak transcription	Small Intestine	intestine
15	chr12:58330200-58334600	Weak transcription	Esophagus	oesophagus
16	chr12:58330200-58334600	Weak transcription	Left Ventricle	heart
17	chr12:58330200-58334600	Weak transcription	Lung	lung
18	chr12:58330200-58334600	Weak transcription	Pancreas	Pancrea
19	chr12:58330200-58334600	Weak transcription	Spleen	Spleen
20	chr12:58330200-58334800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:58330400-58330800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:58330400-58330800	Enhancers	Primary B cells from cord blood	blood
23	chr12:58330400-58330800	Flanking Active TSS	GM12878-XiMat	blood
24	chr12:58330400-58330800	Flanking Active TSS	HepG2	liver
25	chr12:58330400-58331200	Enhancers	Fetal Thymus	thymus
26	chr12:58330400-58332800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:58330400-58334600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:58330400-58334600	Weak transcription	Placenta	Placenta
29	chr12:58330400-58334600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:58330600-58330800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr12:58330600-58330800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr12:58330600-58330800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:58330600-58330800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:58330600-58330800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:58330600-58330800	Active TSS	Liver	Liver
36	chr12:58330600-58330800	Enhancers	Rectal Smooth Muscle	rectum
37	chr12:58330600-58330800	Enhancers	Thymus	Thymus
38	chr12:58330600-58330800	Enhancers	NHEK	skin
39	chr12:58330600-58331600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:58330600-58331600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr12:58330600-58333400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr12:58330600-58333600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:58330600-58333600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:58330600-58333800	Weak transcription	Primary T cells from cord blood	blood
45	chr12:58330600-58333800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:58330600-58334000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:58330600-58334000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:58330600-58334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:58330600-58334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:58330600-58334200	Weak transcription	Primary T cells fromperipheralblood	blood

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