Variant report

Variant	rs3852590
Chromosome Location	chr12:120556208-120556209
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	MXI1	chr12:120556015-120556808	Hela-S3	cervix:	n/a	n/a
4	NFE2	chr12:120556166-120556526	K562	blood:	n/a	chr12:120556339-120556354 chr12:120556341-120556351 chr12:120556340-120556349
5	POLR2A	chr12:120556199-120556532	K562	blood:	n/a	n/a
6	POLR2A	chr12:120556046-120556831	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:120556175-120556735	GM12878	blood:	n/a	n/a
8	USF1	chr12:120556097-120556769	K562	blood:	n/a	chr12:120556635-120556646
9	SP1	chr12:120555715-120556939	A549	lung:	n/a	n/a
10	MYC	chr12:120556058-120556623	K562	blood:	n/a	n/a
11	POLR2A	chr12:120556141-120556584	K562	blood:	n/a	n/a
12	GABPA	chr12:120556106-120556588	MCF-7	breast:	n/a	n/a
13	POLR2A	chr12:120555855-120556837	MCF10A-Er-Src	breast:	n/a	n/a
14	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
15	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
16	SP1	chr12:120556070-120556794	A549	lung:	n/a	n/a
17	POLR2A	chr12:120556198-120556536	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr12:120555765-120556759	A549	lung:	n/a	n/a
19	POLR2A	chr12:120556023-120556882	GM12892	blood:	n/a	n/a
20	TAF1	chr12:120556107-120556463	Hela-S3	cervix:	n/a	n/a
21	MXI1	chr12:120556200-120556807	HepG2	liver:	n/a	n/a
22	MAFF	chr12:120556056-120556575	K562	blood:	n/a	chr12:120556338-120556356
23	STAT3	chr12:120555802-120556858	MCF10A-Er-Src	breast:	n/a	chr12:120556848-120556856
24	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
25	MAX	chr12:120556025-120556827	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:120556033-120556651	Hela-S3	cervix:	n/a	n/a
27	MTA3	chr12:120555921-120558066	GM12878	blood:	n/a	n/a
28	FOS	chr12:120555779-120556848	MCF10A-Er-Src	breast:	n/a	chr12:120556179-120556190 chr12:120556679-120556690 chr12:120556179-120556191
29	MXI1	chr12:120555719-120557083	IMR90	lung:	n/a	n/a
30	MAX	chr12:120556137-120556860	MCF-7	breast:	n/a	n/a
31	MAX	chr12:120555838-120557022	A549	lung:	n/a	n/a
32	MAX	chr12:120555993-120556951	A549	lung:	n/a	n/a
33	GATA3	chr12:120555876-120556246	T-47D	breast:	n/a	chr12:120556179-120556188
34	MAX	chr12:120556166-120556517	H1-hESC	embryonic stem cell:	n/a	n/a
35	EP300	chr12:120555918-120556917	A549	lung:	n/a	chr12:120556822-120556829
36	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
37	BCL3	chr12:120555958-120556924	A549	lung:	n/a	n/a
38	POLR2A	chr12:120556128-120556608	GM12892	blood:	n/a	n/a
39	SIN3AK20	chr12:120556032-120556926	A549	lung:	n/a	n/a
40	FOSL2	chr12:120555811-120556985	A549	lung:	n/a	chr12:120556847-120556856 chr12:120556179-120556190 chr12:120556179-120556191
41	JUND	chr12:120556163-120556772	H1-hESC	embryonic stem cell:	n/a	chr12:120556179-120556190 chr12:120556179-120556191
42	MAX	chr12:120556119-120556525	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:120556182-120556564	GM12891	blood:	n/a	n/a
44	SIX5	chr12:120555819-120556924	A549	lung:	n/a	n/a
45	MYC	chr12:120555908-120556870	MCF10A-Er-Src	breast:	n/a	n/a
46	BACH1	chr12:120556109-120556590	K562	blood:	n/a	n/a
47	POLR2A	chr12:120556058-120556518	GM12891	blood:	n/a	n/a
48	EP300	chr12:120555825-120556937	A549	lung:	n/a	chr12:120556822-120556829
49	IRF1	chr12:120555810-120556849	K562	blood:	n/a	n/a
50	TAF1	chr12:120556138-120556534	H1-hESC	embryonic stem cell:	n/a	n/a

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	chr12:120516359..120519600-chr12:120552938..120556302,7	MCF-7	breast:
8	chr12:120553299..120556376-chr12:120632430..120634315,3	MCF-7	breast:
9	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
10	chr12:120554072..120556853-chr12:120607712..120610177,2	K562	blood:
11	chr12:120553041..120557313-chr12:120636619..120640383,10	K562	blood:
12	chr12:120551105..120556435-chr12:120727138..120732848,13	K562	blood:
13	chr12:120555871..120557729-chr12:120701030..120703971,3	MCF-7	breast:
14	chr12:120551667..120557354-chr12:120726466..120731431,13	MCF-7	breast:
15	chr12:120552903..120558662-chr12:120635855..120639972,12	MCF-7	breast:
16	chr12:120551112..120557922-chr12:120727181..120731830,12	K562	blood:
17	chr12:120553785..120557408-chr12:120702135..120705915,4	K562	blood:
18	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
ENSG00000089157	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000089159	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10492050	1.00[EUR][1000 genomes]
rs12301083	1.00[EUR][1000 genomes]
rs13343210	1.00[EUR][1000 genomes]
rs16949828	1.00[EUR][1000 genomes]
rs16949884	1.00[EUR][1000 genomes]
rs16949890	1.00[EUR][1000 genomes]
rs16949897	1.00[EUR][1000 genomes]
rs2522132	1.00[EUR][1000 genomes]
rs35938105	1.00[EUR][1000 genomes]
rs56792569	1.00[EUR][1000 genomes]
rs59159546	1.00[EUR][1000 genomes]
rs61733796	1.00[EUR][1000 genomes]
rs61753910	1.00[EUR][1000 genomes]
rs7953006	1.00[EUR][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	chr12:120553800-120556400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:120553800-120556400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:120553800-120556400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:120553800-120556800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr12:120554000-120556400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr12:120554000-120556400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:120554000-120556400	Active TSS	Fetal Kidney	kidney
9	chr12:120554000-120556400	Active TSS	A549	lung
10	chr12:120554000-120556400	Active TSS	HMEC	breast
11	chr12:120554000-120556400	Active TSS	NHEK	skin
12	chr12:120554000-120556800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr12:120554200-120556800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:120555000-120556400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:120555200-120556400	Flanking Active TSS	Liver	Liver
16	chr12:120555200-120556400	Flanking Active TSS	Fetal Stomach	stomach
17	chr12:120555200-120556600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr12:120555200-120556600	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr12:120555200-120556600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr12:120555200-120556600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr12:120555200-120556600	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr12:120555200-120556600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:120555200-120556800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:120555200-120556800	Transcr. at gene 5' and 3'	Dnd41	blood
25	chr12:120555400-120556600	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr12:120555400-120556600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr12:120555400-120556600	Flanking Active TSS	Fetal Brain Male	brain
28	chr12:120555400-120556800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr12:120555400-120556800	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr12:120555400-120556800	Flanking Active TSS	Osteobl	bone
31	chr12:120555600-120556400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr12:120555600-120556400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:120555600-120556400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:120555600-120556400	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr12:120555600-120556400	Flanking Active TSS	Fetal Heart	heart
36	chr12:120555600-120556600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:120555600-120556600	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr12:120555600-120556600	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr12:120555600-120557000	Enhancers	Brain Substantia Nigra	brain
40	chr12:120555600-120557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr12:120555800-120556400	Enhancers	Primary hematopoietic stem cells	blood
42	chr12:120555800-120556400	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr12:120555800-120556400	Flanking Active TSS	Fetal Lung	lung
44	chr12:120555800-120556400	Flanking Active TSS	K562	blood
45	chr12:120555800-120556600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr12:120555800-120556600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:120555800-120556600	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr12:120555800-120556600	Enhancers	Fetal Muscle Trunk	muscle
49	chr12:120555800-120556600	Enhancers	Thymus	Thymus
50	chr12:120555800-120556800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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