Variant report

Variant	rs2301883
Chromosome Location	chr12:120556477-120556478
allele	C/T
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	MXI1	chr12:120556194-120556648	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr12:120556064-120556646	K562	blood:	n/a	chr12:120556344-120556355 chr12:120556343-120556354 chr12:120556342-120556356 chr12:120556344-120556355 chr12:120556341-120556350 chr12:120556339-120556354 chr12:120556343-120556354 chr12:120556340-120556350
3	CTCF	chr12:120556380-120556530	AG10803	skin:	n/a	n/a
4	MXI1	chr12:120556015-120556808	Hela-S3	cervix:	n/a	n/a
5	NFE2	chr12:120556166-120556526	K562	blood:	n/a	chr12:120556339-120556354 chr12:120556341-120556351 chr12:120556340-120556349
6	POLR2A	chr12:120556199-120556532	K562	blood:	n/a	n/a
7	POLR2A	chr12:120556046-120556831	SK-N-MC	brain:	n/a	n/a
8	BHLHE40	chr12:120556222-120556848	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:120556175-120556735	GM12878	blood:	n/a	n/a
10	USF1	chr12:120556097-120556769	K562	blood:	n/a	chr12:120556635-120556646
11	SP1	chr12:120555715-120556939	A549	lung:	n/a	n/a
12	MYC	chr12:120556058-120556623	K562	blood:	n/a	n/a
13	POLR2A	chr12:120556141-120556584	K562	blood:	n/a	n/a
14	GABPA	chr12:120556106-120556588	MCF-7	breast:	n/a	n/a
15	POLR2A	chr12:120555855-120556837	MCF10A-Er-Src	breast:	n/a	n/a
16	MAFK	chr12:120556131-120556559	IMR90	lung:	n/a	chr12:120556344-120556355 chr12:120556343-120556354 chr12:120556342-120556356 chr12:120556344-120556355 chr12:120556341-120556350 chr12:120556339-120556354 chr12:120556343-120556354 chr12:120556340-120556350
17	EBF1	chr12:120556215-120556852	GM12878	blood:	n/a	n/a
18	MAFK	chr12:120556137-120556735	HepG2	liver:	n/a	chr12:120556344-120556355 chr12:120556343-120556354 chr12:120556342-120556356 chr12:120556344-120556355 chr12:120556341-120556350 chr12:120556339-120556354 chr12:120556343-120556354 chr12:120556340-120556350
19	POLR2A	chr12:120556220-120556541	A549	lung:	n/a	n/a
20	SP1	chr12:120556070-120556794	A549	lung:	n/a	n/a
21	POLR2A	chr12:120556198-120556536	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr12:120555765-120556759	A549	lung:	n/a	n/a
23	POLR2A	chr12:120556218-120556584	MCF-7	breast:	n/a	n/a
24	POLR2A	chr12:120556023-120556882	GM12892	blood:	n/a	n/a
25	EP300	chr12:120556252-120556497	K562	blood:	n/a	n/a
26	POLR2A	chr12:120556308-120556693	GM12878	blood:	n/a	n/a
27	MXI1	chr12:120556200-120556807	HepG2	liver:	n/a	n/a
28	MAFF	chr12:120556056-120556575	K562	blood:	n/a	chr12:120556338-120556356
29	STAT3	chr12:120555802-120556858	MCF10A-Er-Src	breast:	n/a	chr12:120556848-120556856
30	RCOR1	chr12:120556251-120556702	K562	blood:	n/a	n/a
31	POLR2A	chr12:120556246-120557110	HepG2	liver:	n/a	n/a
32	MAFK	chr12:120555904-120556721	H1-hESC	embryonic stem cell:	n/a	chr12:120556344-120556355 chr12:120556343-120556354 chr12:120556342-120556356 chr12:120556344-120556355 chr12:120556341-120556350 chr12:120556339-120556354 chr12:120556343-120556354 chr12:120556340-120556350
33	MAX	chr12:120556025-120556827	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr12:120556033-120556651	Hela-S3	cervix:	n/a	n/a
35	MTA3	chr12:120555921-120558066	GM12878	blood:	n/a	n/a
36	FOS	chr12:120555779-120556848	MCF10A-Er-Src	breast:	n/a	chr12:120556179-120556190 chr12:120556679-120556690 chr12:120556179-120556191
37	MXI1	chr12:120555719-120557083	IMR90	lung:	n/a	n/a
38	MAX	chr12:120556137-120556860	MCF-7	breast:	n/a	n/a
39	MAX	chr12:120555838-120557022	A549	lung:	n/a	n/a
40	MAX	chr12:120555993-120556951	A549	lung:	n/a	n/a
41	MAX	chr12:120556166-120556517	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:120556327-120556557	H1-hESC	embryonic stem cell:	n/a	n/a
43	EP300	chr12:120555918-120556917	A549	lung:	n/a	chr12:120556822-120556829
44	MAFK	chr12:120556140-120556770	HepG2	liver:	n/a	chr12:120556344-120556355 chr12:120556343-120556354 chr12:120556342-120556356 chr12:120556344-120556355 chr12:120556341-120556350 chr12:120556339-120556354 chr12:120556343-120556354 chr12:120556340-120556350
45	BCL3	chr12:120555958-120556924	A549	lung:	n/a	n/a
46	POLR2A	chr12:120556356-120556494	A549	lung:	n/a	n/a
47	POLR2A	chr12:120556255-120556576	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr12:120556128-120556608	GM12892	blood:	n/a	n/a
49	SIN3AK20	chr12:120556032-120556926	A549	lung:	n/a	n/a
50	FOSL2	chr12:120555811-120556985	A549	lung:	n/a	chr12:120556847-120556856 chr12:120556179-120556190 chr12:120556179-120556191

No.	Distal block	Cell Line	Cell type
1	chr12:120537048..120541245-chr12:120553607..120557723,6	MCF-7	breast:
2	chr12:120552488..120558210-chr12:120630092..120634088,8	MCF-7	breast:
3	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
4	chr12:120554994..120557100-chr12:120637245..120639085,2	MCF-7	breast:
5	chr12:120548888..120559202-chr12:120724492..120734002,35	MCF-7	breast:
6	chr12:120553957..120557976-chr12:120571615..120578270,6	MCF-7	breast:
7	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
8	chr12:120554072..120556853-chr12:120607712..120610177,2	K562	blood:
9	chr12:120553041..120557313-chr12:120636619..120640383,10	K562	blood:
10	chr12:120556435..120559071-chr12:120718655..120721387,2	MCF-7	breast:
11	chr12:120555871..120557729-chr12:120701030..120703971,3	MCF-7	breast:
12	chr12:120551667..120557354-chr12:120726466..120731431,13	MCF-7	breast:
13	chr12:120552903..120558662-chr12:120635855..120639972,12	MCF-7	breast:
14	chr12:120551112..120557922-chr12:120727181..120731830,12	K562	blood:
15	chr12:120553785..120557408-chr12:120702135..120705915,4	K562	blood:
16	chr12:120554030..120557390-chr12:120602676..120607116,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC64-1	chr12:120554711-120556800	NONHSAT031106

Variant related genes	Relation type
RAB35	TF binding region
ENSG00000089159	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs3759398	1.00[MEX][hapmap]
rs6490285	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7135839	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7294967	1.00[AFR][1000 genomes]
rs7307130	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7312244	0.88[LWK][hapmap];0.81[AFR][1000 genomes]
rs7316521	1.00[MEX][hapmap]
rs7954624	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 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	chr12:120553600-120556600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:120553800-120556800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:120554000-120556800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr12:120554200-120556800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:120555200-120556600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr12:120555200-120556600	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr12:120555200-120556600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr12:120555200-120556600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr12:120555200-120556600	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr12:120555200-120556600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr12:120555200-120556800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:120555200-120556800	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr12:120555400-120556600	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr12:120555400-120556600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr12:120555400-120556600	Flanking Active TSS	Fetal Brain Male	brain
16	chr12:120555400-120556800	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr12:120555400-120556800	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr12:120555400-120556800	Flanking Active TSS	Osteobl	bone
19	chr12:120555600-120556600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:120555600-120556600	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr12:120555600-120556600	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr12:120555600-120557000	Enhancers	Brain Substantia Nigra	brain
23	chr12:120555600-120557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:120555800-120556600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr12:120555800-120556600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:120555800-120556600	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr12:120555800-120556600	Enhancers	Fetal Muscle Trunk	muscle
28	chr12:120555800-120556600	Enhancers	Thymus	Thymus
29	chr12:120555800-120556800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:120555800-120556800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:120555800-120556800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:120555800-120556800	Flanking Active TSS	Fetal Brain Female	brain
33	chr12:120555800-120556800	Flanking Active TSS	HUVEC	blood vessel
34	chr12:120555800-120557000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:120555800-120557000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr12:120555800-120557400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr12:120555800-120558000	Enhancers	Primary B cells from cord blood	blood
38	chr12:120555800-120558400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:120555800-120562200	Enhancers	Primary B cells from peripheral blood	blood
40	chr12:120555800-120563800	Weak transcription	Aorta	Aorta
41	chr12:120556000-120556600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:120556000-120556600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:120556000-120556600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:120556000-120556600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr12:120556000-120556600	Enhancers	Fetal Muscle Leg	muscle
46	chr12:120556000-120556600	Enhancers	Fetal Thymus	thymus
47	chr12:120556000-120556600	Flanking Active TSS	HepG2	liver
48	chr12:120556000-120556800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr12:120556000-120556800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr12:120556000-120556800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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