Variant report

Variant	rs58548156
Chromosome Location	chr12:56553940-56553941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:130)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:130 , 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	chr12:56552592-56554130	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	CTCF	chr12:56553642-56554217	T-47D	breast:	n/a	n/a
12	JUND	chr12:56552646-56555329	A549	lung:	n/a	n/a
13	POLR2A	chr12:56551168-56556161	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:56551896-56556539	HCT-116	colon:	n/a	n/a
15	POLR2A	chr12:56551408-56556564	K562	blood:	n/a	n/a
16	POLR2A	chr12:56550856-56557007	HepG2	liver:	n/a	n/a
17	CHD1	chr12:56551947-56555381	IMR90	lung:	n/a	chr12:56552251-56552261 chr12:56554880-56554890
18	POLR2A	chr12:56551369-56560498	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:56551123-56558578	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:56551053-56559864	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:56551393-56557009	K562	blood:	n/a	n/a
22	POLR2A	chr12:56550960-56557121	K562	blood:	n/a	n/a
23	BCL3	chr12:56551157-56556978	A549	lung:	n/a	chr12:56553213-56553222 chr12:56554315-56554324 chr12:56552652-56552661 chr12:56554170-56554179
24	POLR2A	chr12:56551331-56558611	U87	brain:	n/a	n/a
25	POLR2A	chr12:56551292-56558563	HepG2	liver:	n/a	n/a
26	CTCF	chr12:56553920-56554070	HEK293	kidney:	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	chr12:56551288-56555232	K562	blood:	n/a	n/a
30	POLR2A	chr12:56553671-56554519	A549	lung:	n/a	n/a
31	POLR2A	chr12:56553459-56557519	K562	blood:	n/a	n/a
32	POLR2A	chr12:56553752-56553979	A549	lung:	n/a	n/a
33	FOXM1	chr12:56553557-56554471	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:56551184-56558544	GM12878	blood:	n/a	n/a
35	BCL3	chr12:56553704-56554116	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:56550944-56560010	GM12892	blood:	n/a	n/a
37	POLR2A	chr12:56550950-56560311	U87	brain:	n/a	n/a
38	POLR2A	chr12:56550946-56559901	GM12892	blood:	n/a	n/a
39	BCLAF1	chr12:56551949-56554159	GM12878	blood:	n/a	chr12:56553213-56553222 chr12:56552652-56552661
40	CHD1	chr12:56551242-56553943	H1-hESC	embryonic stem cell:	n/a	chr12:56552251-56552261
41	POLR2A	chr12:56553575-56555357	H1-neurons	neurons:	n/a	n/a
42	CCNT2	chr12:56553816-56553996	K562	blood:	n/a	n/a
43	POLR2A	chr12:56550849-56560509	H1-hESC	embryonic stem cell:	n/a	n/a
44	BCL3	chr12:56551316-56554188	A549	lung:	n/a	chr12:56553213-56553222 chr12:56552652-56552661 chr12:56554170-56554179
45	PML	chr12:56553623-56554920	K562	blood:	n/a	chr12:56554129-56554137
46	POLR2A	chr12:56553724-56553969	A549	lung:	n/a	n/a
47	POLR2A	chr12:56551127-56558589	GM18505	blood:	n/a	n/a
48	POLR2A	chr12:56551356-56556024	K562	blood:	n/a	n/a
49	POLR2A	chr12:56551464-56559788	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr12:56551956-56557049	GM12891	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56471332..56475358-chr12:56550630..56554454,5	MCF-7	breast:
2	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
3	chr12:56121253..56122830-chr12:56553054..56555339,2	MCF-7	breast:
4	chr12:56434567..56436421-chr12:56551645..56554362,3	MCF-7	breast:
5	chr12:56551311..56554280-chr12:56613250..56616267,3	MCF-7	breast:
6	chr12:56531568..56534983-chr12:56550075..56554520,6	MCF-7	breast:
7	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:
8	chr12:56549760..56554422-chr12:56650832..56654963,6	MCF-7	breast:
9	chr11:61734073..61736809-chr12:56551929..56554147,2	MCF-7	breast:
10	chr12:56536501..56538802-chr12:56552198..56554579,2	MCF-7	breast:
11	chr12:56529351..56534783-chr12:56551483..56555184,6	MCF-7	breast:
12	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
13	chr12:56497819..56500036-chr12:56550546..56554351,4	MCF-7	breast:
14	chr12:56551520..56554242-chr12:56650975..56653538,2	MCF-7	breast:
15	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
16	chr12:56551730..56554656-chr12:57027945..57032236,3	K562	blood:
17	chr12:56223309..56224865-chr12:56552081..56554400,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257809	TF binding region
MYL6	TF binding region
ENSG00000139645	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000167996	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000269089	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000258199	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10876878	0.83[ASN][1000 genomes]
rs11171752	0.94[ASN][1000 genomes]
rs11171772	0.83[ASN][1000 genomes]
rs11834728	1.00[ASN][1000 genomes]
rs12320265	0.83[ASN][1000 genomes]
rs1274502	0.83[ASN][1000 genomes]
rs1274503	0.83[ASN][1000 genomes]
rs1405859	0.83[ASN][1000 genomes]
rs17118333	1.00[ASN][1000 genomes]
rs2271188	1.00[ASN][1000 genomes]
rs2271190	1.00[ASN][1000 genomes]
rs2271192	0.94[ASN][1000 genomes]
rs2463365	0.83[ASN][1000 genomes]
rs2629451	0.83[ASN][1000 genomes]
rs2629453	0.83[ASN][1000 genomes]
rs2695783	0.83[ASN][1000 genomes]
rs2695784	0.83[ASN][1000 genomes]
rs28676339	1.00[ASN][1000 genomes]
rs2930788	0.83[ASN][1000 genomes]
rs2950573	0.83[ASN][1000 genomes]
rs3759096	1.00[ASN][1000 genomes]
rs3802996	1.00[ASN][1000 genomes]
rs3809130	1.00[ASN][1000 genomes]
rs55887836	0.93[ASN][1000 genomes]
rs56851901	1.00[ASN][1000 genomes]
rs57280585	1.00[ASN][1000 genomes]
rs58009483	0.83[ASN][1000 genomes]
rs58476735	1.00[ASN][1000 genomes]
rs58663297	1.00[ASN][1000 genomes]
rs59053322	0.83[ASN][1000 genomes]
rs59078852	0.83[ASN][1000 genomes]
rs59966703	0.83[ASN][1000 genomes]
rs60396934	1.00[ASN][1000 genomes]
rs61939011	0.83[ASN][1000 genomes]
rs703823	0.83[ASN][1000 genomes]
rs7489249	0.83[ASN][1000 genomes]
rs773654	0.83[ASN][1000 genomes]
rs773658	0.83[ASN][1000 genomes]
rs773659	0.83[ASN][1000 genomes]
rs773661	0.83[ASN][1000 genomes]
rs7962107	0.83[ASN][1000 genomes]
rs7967464	0.83[ASN][1000 genomes]
rs7975405	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv559011	chr12:56551249-56555022	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
3	nsv559012	chr12:56551249-56555360	Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	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
5	nsv559014	chr12:56551250-56555022	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
6	nsv559015	chr12:56551480-56555022	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 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	chr12:56551000-56554400	Active TSS	Ovary	ovary
2	chr12:56551200-56554200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56551400-56554400	Active TSS	Small Intestine	intestine
4	chr12:56552200-56555000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:56552200-56555800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
6	chr12:56552400-56554400	ZNF genes & repeats	Fetal Heart	heart
7	chr12:56552400-56554600	Transcr. at gene 5' and 3'	Fetal Lung	lung
8	chr12:56552400-56554800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
9	chr12:56552400-56555000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
10	chr12:56552400-56555000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
11	chr12:56552400-56555400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
12	chr12:56552600-56555000	Transcr. at gene 5' and 3'	A549	lung
13	chr12:56552600-56555200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:56552600-56555600	Transcr. at gene 5' and 3'	HSMM	muscle
15	chr12:56552800-56554200	Transcr. at gene 5' and 3'	Pancreatic Islets	Pancreatic Islet
16	chr12:56552800-56554600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr12:56552800-56555000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
18	chr12:56552800-56555000	Transcr. at gene 5' and 3'	Thymus	Thymus
19	chr12:56552800-56555400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
20	chr12:56552800-56555800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:56552800-56556000	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
22	chr12:56552800-56556200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:56553000-56554200	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
24	chr12:56553000-56554400	Transcr. at gene 5' and 3'	K562	blood
25	chr12:56553000-56554600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:56553000-56554600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
27	chr12:56553000-56555000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
28	chr12:56553000-56555000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
29	chr12:56553000-56555200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:56553000-56555200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
31	chr12:56553000-56555400	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr12:56553000-56555600	Transcr. at gene 5' and 3'	NHEK	skin
33	chr12:56553000-56555600	Transcr. at gene 5' and 3'	NHLF	lung
34	chr12:56553000-56555600	Transcr. at gene 5' and 3'	Osteobl	bone
35	chr12:56553000-56555800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:56553000-56556200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
37	chr12:56553000-56557000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
38	chr12:56553200-56554000	Transcr. at gene 5' and 3'	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:56553200-56554200	Flanking Active TSS	Fetal Brain Male	brain
40	chr12:56553200-56554400	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
41	chr12:56553200-56554400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:56553200-56554400	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
43	chr12:56553200-56554400	Transcr. at gene 5' and 3'	Spleen	Spleen
44	chr12:56553200-56554600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
45	chr12:56553200-56554600	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:56553200-56554800	Transcr. at gene 5' and 3'	Placenta	Placenta
47	chr12:56553200-56554800	Transcr. at gene 5' and 3'	Stomach Mucosa	stomach
48	chr12:56553200-56554800	Transcr. at gene 5' and 3'	HepG2	liver
49	chr12:56553200-56555000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:56553200-56555000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell

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