Variant report

Variant	rs60419159
Chromosome Location	chr12:56555694-56555695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:107)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:107 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56551094-56558885	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:56554227-56556989	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56551096-56559842	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56551899-56559978	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:56551937-56557019	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:56550969-56558589	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:56551944-56557093	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:56551911-56556101	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr12:56551250-56558611	U87	brain:	n/a	n/a
10	PBX3	chr12:56553571-56556173	SK-N-SH	brain:	n/a	n/a
11	CHD2	chr12:56555687-56555887	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:56555599-56556050	HepG2	liver:	n/a	n/a
13	SP4	chr12:56555563-56556069	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:56551168-56556161	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:56551896-56556539	HCT-116	colon:	n/a	n/a
16	POLR2A	chr12:56551408-56556564	K562	blood:	n/a	n/a
17	POLR2A	chr12:56550856-56557007	HepG2	liver:	n/a	n/a
18	HEY1	chr12:56555154-56555954	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:56551369-56560498	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr12:56551123-56558578	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr12:56551053-56559864	GM12891	blood:	n/a	n/a
22	POLR2A	chr12:56551393-56557009	K562	blood:	n/a	n/a
23	POLR2A	chr12:56550960-56557121	K562	blood:	n/a	n/a
24	BCL3	chr12:56551157-56556978	A549	lung:	n/a	chr12:56553213-56553222 chr12:56554315-56554324 chr12:56552652-56552661 chr12:56554170-56554179
25	POLR2A	chr12:56551331-56558611	U87	brain:	n/a	n/a
26	POLR2A	chr12:56551292-56558563	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:56550957-56556171	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:56551237-56556498	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:56553459-56557519	K562	blood:	n/a	n/a
30	PML	chr12:56555047-56556964	K562	blood:	n/a	n/a
31	POLR2A	chr12:56555404-56558566	HepG2	liver:	n/a	n/a
32	POLR2A	chr12:56551184-56558544	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:56550944-56560010	GM12892	blood:	n/a	n/a
34	POLR2A	chr12:56550950-56560311	U87	brain:	n/a	n/a
35	POLR2A	chr12:56550946-56559901	GM12892	blood:	n/a	n/a
36	POLR2A	chr12:56554720-56555844	HEK293	kidney:	n/a	n/a
37	POLR2A	chr12:56550849-56560509	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr12:56555679-56555768	A549	lung:	n/a	n/a
39	POLR2A	chr12:56551127-56558589	GM18505	blood:	n/a	n/a
40	POLR2A	chr12:56551356-56556024	K562	blood:	n/a	n/a
41	PBX3	chr12:56555353-56556477	A549	lung:	n/a	n/a
42	POLR2A	chr12:56555410-56556143	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr12:56551464-56559788	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr12:56551956-56557049	GM12891	blood:	n/a	n/a
45	POLR2A	chr12:56551345-56560303	MCF10A-Er-Src	breast:	n/a	n/a
46	CHD2	chr12:56555565-56557660	H1-hESC	embryonic stem cell:	n/a	n/a
47	TCF12	chr12:56554692-56556257	A549	lung:	n/a	n/a
48	POLR2A	chr12:56551917-56557084	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr12:56551440-56558535	HepG2	liver:	n/a	n/a
50	PML	chr12:56550940-56558565	GM12878	blood:	n/a	chr12:56554129-56554137

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56519569..56524417-chr12:56555136..56559386,7	MCF-7	breast:
2	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
3	chr12:56555640..56556592-chr5:77382006..77382689,2	MCF-7	breast:
4	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
5	chr12:56108963..56111189-chr12:56554025..56556182,2	MCF-7	breast:
6	chr12:56555575..56559799-chr12:56572215..56575124,4	MCF-7	breast:
7	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
8	chr12:56554308..56556384-chr12:56600666..56602668,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYL6-2	chr12:56555565-56556115	NONHSAT028784

No data

Variant related genes	Relation type
ENSG00000257809	TF binding region
ENSG00000135424	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000258311	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000135441	Chromatin interaction
ENSG00000258199	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11834038	1.00[AMR][1000 genomes]
rs11835054	1.00[AMR][1000 genomes]
rs1508211	1.00[AMR][1000 genomes]
rs2066812	1.00[AMR][1000 genomes]
rs2271195	1.00[AMR][1000 genomes]
rs35807059	1.00[AMR][1000 genomes]
rs55771348	1.00[AMR][1000 genomes]
rs56983027	1.00[AMR][1000 genomes]
rs61186183	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61695444	1.00[AMR][1000 genomes]
rs73338396	1.00[AMR][1000 genomes]
rs73338402	1.00[AMR][1000 genomes]
rs74091499	1.00[AMR][1000 genomes]
rs74092004	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74092007	1.00[AMR][1000 genomes]
rs74092015	1.00[AMR][1000 genomes]
rs74094517	1.00[AMR][1000 genomes]
rs74094520	1.00[AMR][1000 genomes]
rs74094521	1.00[AMR][1000 genomes]
rs74094522	1.00[AMR][1000 genomes]
rs74094539	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv559013	chr12:56551249-56556389	Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56552200-56555800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr12:56552800-56555800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:56552800-56556000	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
4	chr12:56552800-56556200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:56553000-56555800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:56553000-56556200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
7	chr12:56553000-56557000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
8	chr12:56553200-56555800	Transcr. at gene 5' and 3'	NH-A	brain
9	chr12:56553200-56556800	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
10	chr12:56553200-56557800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:56553400-56556000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
12	chr12:56553600-56555800	Transcr. at gene 5' and 3'	Right Ventricle	heart
13	chr12:56553800-56555800	Genic enhancers	Placenta Amnion	Placenta Amnion
14	chr12:56554000-56557400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56554000-56582000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:56554200-56556600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:56554200-56581400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:56554600-56555800	Genic enhancers	Brain Angular Gyrus	brain
19	chr12:56554600-56555800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
20	chr12:56554600-56556800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:56554600-56557400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:56554600-56557600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:56554600-56558200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:56554600-56568600	Strong transcription	Ovary	ovary
25	chr12:56554800-56555800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr12:56554800-56555800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr12:56554800-56555800	Genic enhancers	Brain Hippocampus Middle	brain
28	chr12:56554800-56555800	Genic enhancers	HepG2	liver
29	chr12:56554800-56556000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:56554800-56556000	Genic enhancers	Fetal Intestine Large	intestine
31	chr12:56554800-56556000	Genic enhancers	Pancreas	Pancrea
32	chr12:56554800-56556600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:56554800-56556600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:56554800-56557600	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:56555000-56555800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:56555000-56555800	Genic enhancers	Fetal Thymus	thymus
37	chr12:56555000-56556000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:56555000-56556000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:56555000-56556200	Genic enhancers	Fetal Intestine Small	intestine
40	chr12:56555000-56556400	Strong transcription	HSMMtube	muscle
41	chr12:56555000-56556600	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr12:56555000-56556600	Strong transcription	Psoas Muscle	Psoas
43	chr12:56555000-56556800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:56555000-56556800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr12:56555000-56556800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr12:56555000-56557200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:56555000-56557400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr12:56555000-56557600	Genic enhancers	Fetal Muscle Leg	muscle
49	chr12:56555000-56557800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr12:56555000-56558400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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