Variant report

Variant	rs12304483
Chromosome Location	chr12:49657998-49657999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:51)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:49657944-49659770	HCT-116	colon:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
2	POLR2A	chr12:49657883-49658343	U87	brain:	n/a	n/a
3	MYC	chr12:49657953-49660107	A549	lung:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
4	MTA3	chr12:49657994-49659777	GM12878	blood:	n/a	n/a
5	FOXM1	chr12:49657916-49659811	ECC-1	luminal epithelium:	n/a	n/a
6	NR2F2	chr12:49657924-49659910	K562	blood:	n/a	n/a
7	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
8	JUN	chr12:49657870-49659973	K562	blood:	n/a	chr12:49659157-49659171 chr12:49659434-49659444 chr12:49659301-49659315 chr12:49658704-49658713 chr12:49659434-49659444 chr12:49659434-49659444 chr12:49659268-49659277 chr12:49659435-49659443 chr12:49659433-49659445 chr12:49658253-49658262
9	TCF12	chr12:49657946-49659647	ECC-1	luminal epithelium:	n/a	n/a
10	PML	chr12:49657967-49660093	GM12878	blood:	n/a	n/a
11	ZNF384	chr12:49657865-49658315	K562	blood:	n/a	n/a
12	MAZ	chr12:49657950-49659883	IMR90	lung:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
13	POLR2A	chr12:49657881-49662104	U87	brain:	n/a	n/a
14	POLR2A	chr12:49657892-49662191	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr12:49657919-49660000	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr12:49657998-49661215	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr12:49657989-49660000	ECC-1	luminal epithelium:	n/a	n/a
18	HCFC1	chr12:49657918-49661243	Hela-S3	cervix:	n/a	n/a
19	TCF12	chr12:49657973-49659814	ECC-1	luminal epithelium:	n/a	n/a
20	GATA1	chr12:49657941-49659930	PBDE	blood:	n/a	n/a
21	E2F6	chr12:49657985-49658473	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOSL2	chr12:49657938-49660023	A549	lung:	n/a	chr12:49659157-49659171 chr12:49659434-49659444 chr12:49659301-49659315 chr12:49659434-49659445 chr12:49658704-49658713 chr12:49659434-49659444 chr12:49659434-49659444 chr12:49659268-49659277 chr12:49659435-49659443 chr12:49659433-49659445 chr12:49658253-49658262
23	MAX	chr12:49657317-49659785	HCT-116	colon:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
24	MAX	chr12:49657924-49659990	A549	lung:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
25	MAX	chr12:49657952-49659730	ECC-1	luminal epithelium:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
26	FOXM1	chr12:49657890-49659826	ECC-1	luminal epithelium:	n/a	n/a
27	CHD1	chr12:49657927-49660024	IMR90	lung:	n/a	chr12:49658377-49658387
28	POLR2A	chr12:49657200-49661932	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr12:49657988-49660045	HCT-116	colon:	n/a	n/a

No data

(count:51 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr12:49657860..49660302-chr12:49730399..49733232,3	K562	blood:
2	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
3	chr12:49523107..49527860-chr12:49656151..49664210,14	MCF-7	breast:
4	chr12:49519590..49527322-chr12:49655772..49662610,57	K562	blood:
5	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
6	chr12:49581145..49584248-chr12:49657471..49660758,4	K562	blood:
7	chr12:49462455..49464108-chr12:49657502..49660398,3	K562	blood:
8	chr12:49657320..49660807-chr12:49714613..49719662,6	K562	blood:
9	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
10	chr12:49483859..49487327-chr12:49657616..49660606,5	K562	blood:
11	chr12:49519914..49528393-chr12:49656527..49662615,75	K562	blood:
12	chr12:49501897..49506471-chr12:49657604..49660787,6	MCF-7	breast:
13	chr12:49657692..49659587-chr12:49716247..49718208,2	MCF-7	breast:
14	chr12:49656786..49659396-chr6:114291007..114293085,2	MCF-7	breast:
15	chr12:49499760..49506124-chr12:49657415..49661017,8	K562	blood:
16	chr12:49462406..49465445-chr12:49657502..49661212,4	K562	blood:
17	chr12:49207714..49211177-chr12:49657864..49661147,3	K562	blood:
18	chr12:49657748..49660512-chr12:49730264..49732689,3	MCF-7	breast:
19	chr12:49412238..49414069-chr12:49657738..49659294,2	MCF-7	breast:
20	chr12:49657699..49660591-chr12:49932809..49935394,2	MCF-7	breast:
21	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
22	chr12:49657602..49660330-chr12:50012266..50014334,2	K562	blood:
23	chr11:58875233..58875940-chr12:49657802..49658323,2	Hela-S3	cervix:
24	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:
25	chr12:49496967..49499814-chr12:49657721..49660285,2	MCF-7	breast:
26	chr12:49390613..49393583-chr12:49657516..49659698,3	K562	blood:
27	chr12:49656589..49659420-chr13:91999028..92001178,2	K562	blood:
28	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
29	chr12:49657419..49659044-chr4:71567380..71569012,2	MCF-7	breast:
30	chr12:49109310..49111237-chr12:49657606..49659331,2	K562	blood:
31	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
32	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
33	chr12:49410141..49415550-chr12:49657481..49661686,9	K562	blood:
34	chr12:49580809..49583875-chr12:49657471..49661424,5	K562	blood:
35	chr12:49216477..49218996-chr12:49657402..49659438,2	K562	blood:
36	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
37	chr12:49522979..49526796-chr12:49655970..49661455,13	MCF-7	breast:
38	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
39	chr12:49657208..49661363-chr12:49714955..49717990,5	MCF-7	breast:
40	chr12:49453115..49455291-chr12:49657846..49660975,4	MCF-7	breast:
41	chr12:49657502..49660502-chr12:50135111..50136880,4	K562	blood:
42	chr12:49581100..49585285-chr12:49656726..49660800,10	MCF-7	breast:
43	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
44	chr12:49410741..49414968-chr12:49656213..49660641,6	K562	blood:
45	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
46	chr11:126136855..126139386-chr12:49657857..49660663,2	MCF-7	breast:
47	chr12:49657477..49660356-chr12:49930384..49933439,3	K562	blood:
48	chr12:49657182..49662198-chr12:49738070..49742868,13	MCF-7	breast:
49	chr12:49580754..49584871-chr12:49657957..49661825,4	MCF-7	breast:
50	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:

No data

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000181929	Chromatin interaction
ENSG00000228624	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000181418	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000207058	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000110074	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000258104	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000207448	Chromatin interaction
ENSG00000196591	Chromatin interaction
ENSG00000182934	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10047512	1.00[AMR][1000 genomes]
rs10047588	1.00[AMR][1000 genomes]
rs1109811	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168925	1.00[AMR][1000 genomes]
rs11168927	1.00[AMR][1000 genomes]
rs11168928	1.00[AMR][1000 genomes]
rs11168931	1.00[AMR][1000 genomes]
rs11168938	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168940	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168952	0.86[AFR][1000 genomes]
rs11168954	0.86[AFR][1000 genomes]
rs11168955	0.83[AFR][1000 genomes]
rs11168956	0.94[AFR][1000 genomes]
rs11168957	0.94[AFR][1000 genomes]
rs11168958	0.94[AFR][1000 genomes]
rs12296231	1.00[AMR][1000 genomes]
rs12296536	1.00[AMR][1000 genomes]
rs12297433	1.00[AMR][1000 genomes]
rs12300386	1.00[AMR][1000 genomes]
rs12300998	1.00[AMR][1000 genomes]
rs12304259	1.00[AMR][1000 genomes]
rs12304746	1.00[AMR][1000 genomes]
rs12308571	0.94[AFR][1000 genomes]
rs12309028	1.00[AMR][1000 genomes]
rs12310093	0.86[AFR][1000 genomes]
rs12314967	1.00[AMR][1000 genomes]
rs12318666	1.00[AMR][1000 genomes]
rs12322876	1.00[AMR][1000 genomes]
rs28758893	1.00[AMR][1000 genomes]
rs3759170	0.86[AFR][1000 genomes]
rs9804936	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49650000-49658000	Weak transcription	Right Atrium	heart
2	chr12:49652200-49658000	Weak transcription	Fetal Brain Female	brain
3	chr12:49653600-49658000	Weak transcription	Fetal Kidney	kidney
4	chr12:49654200-49658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:49654600-49658000	Weak transcription	Aorta	Aorta
6	chr12:49654800-49658000	Weak transcription	Ovary	ovary
7	chr12:49655000-49658000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:49655000-49658200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:49656800-49658000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:49657000-49658000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:49657000-49658000	Enhancers	Spleen	Spleen
12	chr12:49657000-49660200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:49657000-49660200	Active TSS	HSMM	muscle
14	chr12:49657200-49658000	Enhancers	Adipose Nuclei	Adipose
15	chr12:49657200-49659000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:49657200-49659600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:49657200-49660200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:49657200-49660400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr12:49657200-49660600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:49657400-49658000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:49657400-49658200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:49657400-49658200	Enhancers	Fetal Heart	heart
23	chr12:49657400-49659000	Bivalent Enhancer	Fetal Brain Male	brain
24	chr12:49657400-49659400	Active TSS	Rectal Smooth Muscle	rectum
25	chr12:49657400-49659800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:49657400-49660200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:49657600-49658000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:49657600-49658000	Enhancers	Primary B cells from cord blood	blood
29	chr12:49657600-49658000	Enhancers	Primary B cells from peripheral blood	blood
30	chr12:49657600-49658000	Active TSS	Primary hematopoietic stem cells	blood
31	chr12:49657600-49658000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:49657600-49658000	Active TSS	Brain Germinal Matrix	brain
33	chr12:49657600-49658000	Enhancers	Fetal Muscle Leg	muscle
34	chr12:49657600-49658000	Flanking Active TSS	Placenta	Placenta
35	chr12:49657600-49658000	Enhancers	Pancreas	Pancrea
36	chr12:49657600-49658000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr12:49657600-49658000	Active TSS	Thymus	Thymus
38	chr12:49657600-49658200	Active TSS	Psoas Muscle	Psoas
39	chr12:49657600-49658200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr12:49657600-49659400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:49657600-49659600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr12:49657600-49659800	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr12:49657600-49659800	Active TSS	HMEC	breast
44	chr12:49657600-49660000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:49657600-49660200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:49657600-49660400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:49657600-49660400	Active TSS	NHDF-Ad	bronchial
48	chr12:49657600-49660400	Active TSS	NHLF	lung
49	chr12:49657600-49660600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:49657600-49660600	Active TSS	iPS-18 Cell Line	embryonic stem cell

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