Variant report

Variant	rs542729206
Chromosome Location	chr12:49412711-49412712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:503)
CpG islands
(count:0)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:503 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49411737-49413103	Raji	blood:	n/a	n/a
2	YY1	chr12:49412266-49412833	K562	blood:	n/a	n/a
3	IRF1	chr12:49412304-49413119	K562	blood:	n/a	n/a
4	EP300	chr12:49412307-49413066	A549	lung:	n/a	n/a
5	TBP	chr12:49412351-49412927	HepG2	liver:	n/a	n/a
6	HEY1	chr12:49411980-49412948	K562	blood:	n/a	n/a
7	MYC	chr12:49412422-49412799	MCF10A-Er-Src	breast:	n/a	n/a
8	ELF1	chr12:49412303-49412812	A549	lung:	n/a	n/a
9	YY1	chr12:49412174-49413041	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr12:49412308-49412998	HepG2	liver:	n/a	n/a
11	TBL1XR1	chr12:49411819-49412957	K562	blood:	n/a	n/a
12	SPI1	chr12:49412409-49412767	GM12878	blood:	n/a	n/a
13	GABPA	chr12:49411937-49413076	MCF-7	breast:	n/a	n/a
14	CREB1	chr12:49411906-49413153	HepG2	liver:	n/a	n/a
15	TAF1	chr12:49411995-49412948	MCF-7	breast:	n/a	n/a
16	SP1	chr12:49412390-49412814	GM12878	blood:	n/a	chr12:49412576-49412587 chr12:49412607-49412618
17	GABPA	chr12:49412218-49412892	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:49412110-49413113	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr12:49411891-49413127	H1-hESC	embryonic stem cell:	n/a	n/a
20	STAT3	chr12:49412650-49412756	MCF10A-Er-Src	breast:	n/a	n/a
21	REST	chr12:49412389-49412807	SK-N-SH	brain:	n/a	n/a
22	RFX5	chr12:49412353-49412712	HepG2	liver:	n/a	n/a
23	ZMIZ1	chr12:49412258-49412878	K562	blood:	n/a	n/a
24	YY1	chr12:49412106-49412851	A549	lung:	n/a	n/a
25	MAZ	chr12:49412292-49413514	K562	blood:	n/a	n/a
26	ELF1	chr12:49412324-49412887	HepG2	liver:	n/a	n/a
27	ZNF143	chr12:49412335-49412804	Hela-S3	cervix:	n/a	n/a
28	MAX	chr12:49412230-49413075	MCF-7	breast:	n/a	n/a
29	RCOR1	chr12:49412335-49412971	GM12878	blood:	n/a	n/a
30	MAX	chr12:49411634-49413032	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr12:49411681-49413024	Hela-S3	cervix:	n/a	n/a
32	REST	chr12:49411786-49413051	A549	lung:	n/a	n/a
33	TAF1	chr12:49412295-49412812	GM12892	blood:	n/a	n/a
34	TAF1	chr12:49412211-49412796	SK-N-SH	brain:	n/a	n/a
35	USF2	chr12:49412139-49412969	GM12878	blood:	n/a	n/a
36	TBL1XR1	chr12:49412317-49413080	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:49411457-49413584	HUVEC	blood vessel:	n/a	n/a
38	ELK4	chr12:49412408-49412769	HEK293	kidney:	n/a	chr12:49412604-49412615 chr12:49412659-49412670
39	RCOR1	chr12:49411916-49412976	K562	blood:	n/a	n/a
40	REST	chr12:49412237-49412786	PFSK-1	brain:	n/a	n/a
41	RUNX3	chr12:49412243-49413063	GM12878	blood:	n/a	n/a
42	E2F4	chr12:49412606-49412940	GM12878	blood:	n/a	n/a
43	RAD21	chr12:49412478-49413030	A549	lung:	n/a	n/a
44	POLR2A	chr12:49411738-49413078	GM15510	blood:	n/a	n/a
45	TBP	chr12:49412313-49412993	GM12878	blood:	n/a	n/a
46	SIN3AK20	chr12:49412184-49412797	PFSK-1	brain:	n/a	n/a
47	E2F6	chr12:49412060-49413150	A549	lung:	n/a	n/a
48	TAF1	chr12:49412287-49412819	GM12892	blood:	n/a	n/a
49	ZBTB33	chr12:49412249-49412850	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr12:49411538-49413120	K562	blood:	n/a	n/a

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49411250..49414905-chr12:49447359..49450802,6	MCF-7	breast:
2	chr12:49412133..49412956-chr20:47894836..47895476,2	Hela-S3	cervix:
3	chr12:49412124..49413026-chr5:32174262..32174852,2	Hela-S3	cervix:
4	chr12:49408415..49414757-chr12:49522619..49525582,9	MCF-7	breast:
5	chr12:49410741..49414968-chr12:49656213..49660641,6	K562	blood:
6	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
7	chr12:49348804..49352502-chr12:49411258..49414497,4	MCF-7	breast:
8	chr12:49412238..49414069-chr12:49657738..49659294,2	MCF-7	breast:
9	chr12:49349202..49351999-chr12:49410599..49414055,4	MCF-7	breast:
10	chr1:28832099..28833043-chr12:49412456..49412982,2	Hela-S3	cervix:
11	chr12:49412434..49414037-chr12:49481965..49485048,3	K562	blood:
12	chr12:49368203..49373775-chr12:49410781..49415457,6	K562	blood:
13	chr12:49412487..49413124-chr3:195808419..195809056,2	Hela-S3	cervix:
14	chr12:49388402..49390811-chr12:49410964..49413711,2	MCF-7	breast:
15	chr12:49207853..49210267-chr12:49412242..49414195,2	K562	blood:
16	chr12:49244558..49246896-chr12:49411138..49413434,2	MCF-7	breast:
17	chr12:49349516..49351260-chr12:49410887..49413470,2	K562	blood:
18	chr12:49412316..49413094-chr19:3606438..3606974,2	Hela-S3	cervix:
19	chr12:49410733..49415536-chr12:49523564..49526910,8	K562	blood:
20	chr12:49412176..49413113-chr15:75746855..75747416,2	Hela-S3	cervix:
21	chr12:49412487..49414498-chr12:49429302..49431280,2	MCF-7	breast:
22	chr12:49410579..49413468-chr12:49666098..49668038,2	K562	blood:
23	chr12:49369680..49374710-chr12:49411684..49416052,5	K562	blood:
24	chr12:49411035..49414032-chr12:49431081..49434275,3	K562	blood:
25	chr12:49109260..49113049-chr12:49411417..49414170,4	K562	blood:
26	chr12:49409658..49414587-chr12:49499656..49504173,4	K562	blood:
27	chr12:49409714..49416851-chr12:49447402..49455499,24	MCF-7	breast:
28	chr12:49407466..49416688-chr12:49451532..49456163,12	MCF-7	breast:
29	chr12:49412260..49412838-chr12:93835928..93836641,2	Hela-S3	cervix:
30	chr12:49411929..49413687-chr17:57923911..57925440,2	MCF-7	breast:
31	chr12:49411020..49415552-chr12:49523211..49527183,13	K562	blood:
32	chr12:49410141..49415550-chr12:49657481..49661686,9	K562	blood:
33	chr12:49209305..49214344-chr12:49410836..49414443,6	MCF-7	breast:
34	chr12:49412361..49413149-chr5:79551650..79552467,2	Hela-S3	cervix:
35	chr12:49410463..49414527-chr12:49462417..49465664,5	K562	blood:
36	chr12:49409906..49413174-chr12:49495482..49498237,3	K562	blood:
37	chr12:49412128..49415221-chr12:49522907..49525212,5	MCF-7	breast:

No data

Variant related genes	Relation type
PRKAG1	TF binding region
ENSG00000177889	Chromatin interaction
ENSG00000164300	Chromatin interaction
ENSG00000125084	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000242125	Chromatin interaction
ENSG00000124201	Chromatin interaction
ENSG00000200303	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000072274	Chromatin interaction
ENSG00000272086	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000258283	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000006638	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000113384	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000177410	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000258101	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
6	esv3387384	chr12:49412035-49416433	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	38 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	chr12:49411200-49413200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:49411400-49412800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:49411400-49413200	Active TSS	Fetal Muscle Trunk	muscle
4	chr12:49411400-49413200	Active TSS	Psoas Muscle	Psoas
5	chr12:49411400-49413200	Active TSS	NHLF	lung
6	chr12:49411400-49413600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:49411600-49413000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:49411600-49413000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:49411600-49413000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:49411600-49413000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:49411600-49413000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:49411600-49413000	Active TSS	Aorta	Aorta
13	chr12:49411600-49413000	Active TSS	Esophagus	oesophagus
14	chr12:49411600-49413200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr12:49411600-49413200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:49411600-49413200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:49411600-49413200	Active TSS	Left Ventricle	heart
18	chr12:49411800-49412800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:49411800-49412800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:49411800-49412800	Active TSS	Brain Hippocampus Middle	brain
21	chr12:49411800-49412800	Active TSS	NH-A	brain
22	chr12:49411800-49412800	Active TSS	NHEK	skin
23	chr12:49411800-49412800	Active TSS	Osteobl	bone
24	chr12:49411800-49413000	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr12:49411800-49413200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:49411800-49413200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr12:49411800-49413200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:49411800-49413200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:49411800-49413200	Active TSS	Fetal Intestine Small	intestine
30	chr12:49411800-49413200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr12:49411800-49413200	Active TSS	Ovary	ovary
32	chr12:49411800-49413200	Active TSS	A549	lung
33	chr12:49411800-49413200	Active TSS	HSMMtube	muscle
34	chr12:49411800-49413200	Active TSS	NHDF-Ad	bronchial
35	chr12:49411800-49413400	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr12:49411800-49413400	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr12:49412000-49412800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:49412000-49412800	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr12:49412000-49412800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:49412000-49412800	Active TSS	Muscle Satellite Cultured Cells	--
41	chr12:49412000-49412800	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr12:49412000-49412800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:49412000-49412800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:49412000-49412800	Active TSS	Fetal Lung	lung
45	chr12:49412000-49412800	Active TSS	Fetal Muscle Leg	muscle
46	chr12:49412000-49412800	Active TSS	Placenta	Placenta
47	chr12:49412000-49412800	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr12:49412000-49412800	Active TSS	Dnd41	blood
49	chr12:49412000-49412800	Active TSS	Hela-S3	cervix
50	chr12:49412000-49412800	Bivalent/Poised TSS	HepG2	liver

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