Variant report

Variant	rs73410881
Chromosome Location	chr12:120555566-120555567
allele	A/G
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	POLR2A	chr12:120555079-120555639	GM12892	blood:	n/a	n/a
2	RUNX3	chr12:120554408-120555625	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:120554368-120555710	H1-hESC	embryonic stem cell:	n/a	n/a
4	MTA3	chr12:120554310-120555833	GM12878	blood:	n/a	n/a
5	MAX	chr12:120553643-120555735	A549	lung:	n/a	chr12:120554993-120555003
6	MAX	chr12:120554466-120555616	H1-hESC	embryonic stem cell:	n/a	chr12:120554993-120555003
7	POLR2A	chr12:120554030-120555603	GM18951	blood:	n/a	n/a
8	MXI1	chr12:120554481-120555649	Hela-S3	cervix:	n/a	chr12:120555481-120555490
9	POLR2A	chr12:120553814-120555709	HepG2	liver:	n/a	n/a
10	MAFK	chr12:120555510-120555629	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:120553844-120555622	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:120554061-120555638	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr12:120554040-120555629	GM12892	blood:	n/a	n/a
14	MAX	chr12:120553803-120555577	HepG2	liver:	n/a	chr12:120554993-120555003
15	WRNIP1	chr12:120555190-120555816	GM12878	blood:	n/a	n/a
16	MAX	chr12:120553852-120555591	ECC-1	luminal epithelium:	n/a	chr12:120554993-120555003
17	SMC3	chr12:120555257-120555673	GM12878	blood:	n/a	n/a
18	SIN3A	chr12:120553907-120555858	H1-hESC	embryonic stem cell:	n/a	chr12:120555150-120555163 chr12:120555077-120555090
19	POLR2A	chr12:120554344-120555901	GM12891	blood:	n/a	n/a
20	POLR2A	chr12:120553918-120555589	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:120554372-120555607	GM12891	blood:	n/a	n/a
22	MAX	chr12:120553803-120555592	K562	blood:	n/a	chr12:120554993-120555003
23	MAX	chr12:120554326-120555589	ECC-1	luminal epithelium:	n/a	chr12:120554993-120555003
24	PML	chr12:120554313-120555716	GM12878	blood:	n/a	n/a
25	MAZ	chr12:120553664-120555812	IMR90	lung:	n/a	chr12:120554993-120555003
26	POLR2A	chr12:120554293-120555589	GM12878	blood:	n/a	n/a
27	SIN3AK20	chr12:120554167-120555709	MCF-7	breast:	n/a	n/a
28	ELF1	chr12:120554309-120555570	GM12878	blood:	n/a	chr12:120554996-120555008 chr12:120554703-120554715
29	POLR2A	chr12:120553828-120555661	GM12892	blood:	n/a	n/a
30	SP1	chr12:120554356-120555656	A549	lung:	n/a	chr12:120555044-120555053 chr12:120555044-120555053 chr12:120554647-120554657 chr12:120555044-120555054 chr12:120554646-120554658 chr12:120554959-120554971 chr12:120554647-120554656 chr12:120555065-120555074 chr12:120554960-120554969 chr12:120554959-120554971 chr12:120554960-120554970 chr12:120555063-120555075 chr12:120554594-120554608 chr12:120554961-120554970 chr12:120555045-120555054 chr12:120555063-120555075 chr12:120555043-120555055 chr12:120554646-120554658 chr12:120554648-120554657 chr12:120554961-120554970 chr12:120554995-120555009 chr12:120555044-120555058 chr12:120555043-120555055 chr12:120554647-120554656 chr12:120555064-120555074
31	CHD1	chr12:120555170-120555973	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZEB1	chr12:120555170-120555624	GM12878	blood:	n/a	n/a
33	GATA3	chr12:120554306-120556859	A549	lung:	n/a	chr12:120554932-120554942 chr12:120556179-120556188
34	POLR2A	chr12:120554000-120555672	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:120554303-120555654	GM12892	blood:	n/a	n/a
36	POLR2A	chr12:120553952-120555646	GM19099	blood:	n/a	n/a
37	BCL3	chr12:120554522-120555739	A549	lung:	n/a	chr12:120555156-120555169 chr12:120554609-120554622 chr12:120554525-120554538 chr12:120555031-120555040 chr12:120554615-120554624 chr12:120554586-120554595
38	E2F6	chr12:120554404-120555568	A549	lung:	n/a	chr12:120554614-120554624 chr12:120555118-120555127 chr12:120555346-120555355 chr12:120554589-120554598 chr12:120555080-120555090 chr12:120554611-120554621 chr12:120554726-120554735 chr12:120554663-120554672 chr12:120554640-120554652
39	POLR2A	chr12:120554022-120555577	GM19193	blood:	n/a	n/a
40	BCLAF1	chr12:120554701-120555751	GM12878	blood:	n/a	chr12:120555156-120555169 chr12:120555031-120555040
41	POLR2A	chr12:120553974-120556007	GM18505	blood:	n/a	n/a
42	MAX	chr12:120553821-120555672	HepG2	liver:	n/a	chr12:120554993-120555003
43	POLR2A	chr12:120554407-120555687	GM12891	blood:	n/a	n/a
44	ATF2	chr12:120555196-120555664	GM12878	blood:	n/a	n/a
45	MXI1	chr12:120554390-120555669	GM12878	blood:	n/a	chr12:120555481-120555490
46	STAT5A	chr12:120554619-120555727	GM12878	blood:	n/a	chr12:120555506-120555517
47	CHD1	chr12:120554457-120555981	GM12878	blood:	n/a	chr12:120555159-120555169 chr12:120554646-120554656
48	MXI1	chr12:120552785-120555717	IMR90	lung:	n/a	chr12:120555481-120555490
49	POLR2A	chr12:120554227-120555701	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr12:120554434-120555652	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120552974..120555854-chr12:120934971..120936620,2	K562	blood:
2	chr12:120537048..120541245-chr12:120553607..120557723,6	MCF-7	breast:
3	chr12:120552488..120558210-chr12:120630092..120634088,8	MCF-7	breast:
4	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
5	chr12:120554994..120557100-chr12:120637245..120639085,2	MCF-7	breast:
6	chr12:120548888..120559202-chr12:120724492..120734002,35	MCF-7	breast:
7	chr12:120553957..120557976-chr12:120571615..120578270,6	MCF-7	breast:
8	chr12:120534104..120540073-chr12:120552292..120555790,7	K562	blood:
9	chr12:120516359..120519600-chr12:120552938..120556302,7	MCF-7	breast:
10	chr12:120553299..120556376-chr12:120632430..120634315,3	MCF-7	breast:
11	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
12	chr12:120554072..120556853-chr12:120607712..120610177,2	K562	blood:
13	chr12:120553041..120557313-chr12:120636619..120640383,10	K562	blood:
14	chr12:120551105..120556435-chr12:120727138..120732848,13	K562	blood:
15	chr12:120552161..120556177-chr12:120630368..120635589,11	K562	blood:
16	chr12:120551667..120557354-chr12:120726466..120731431,13	MCF-7	breast:
17	chr12:120552903..120558662-chr12:120635855..120639972,12	MCF-7	breast:
18	chr12:120551112..120557922-chr12:120727181..120731830,12	K562	blood:
19	chr12:120553785..120557408-chr12:120702135..120705915,4	K562	blood:
20	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
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000111737	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs57754755	1.00[AFR][1000 genomes]
rs58514835	1.00[AFR][1000 genomes]
rs59207263	1.00[AFR][1000 genomes]
rs60106205	1.00[AFR][1000 genomes]
rs60553526	1.00[AFR][1000 genomes]
rs60656828	1.00[AFR][1000 genomes]
rs60723082	1.00[AFR][1000 genomes]
rs61291824	1.00[AFR][1000 genomes]
rs73410890	1.00[AFR][1000 genomes]
rs73410893	1.00[AFR][1000 genomes]
rs73410899	1.00[AFR][1000 genomes]
rs73410901	1.00[AFR][1000 genomes]
rs73412805	1.00[AFR][1000 genomes]
rs73412808	1.00[AFR][1000 genomes]
rs73412809	1.00[AFR][1000 genomes]
rs73412816	1.00[AFR][1000 genomes]
rs73412864	1.00[AFR][1000 genomes]
rs73412896	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	esv3408817	chr12:120553094-120555942	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv3345428	chr12:120553419-120556067	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr12:120553400-120555800	Active TSS	Aorta	Aorta
2	chr12:120553400-120556000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:120553600-120555600	Active TSS	Fetal Muscle Trunk	muscle
4	chr12:120553600-120555600	Active TSS	Gastric	stomach
5	chr12:120553600-120555800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:120553600-120555800	Active TSS	Ovary	ovary
7	chr12:120553600-120556000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr12:120553600-120556000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr12:120553600-120556200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:120553600-120556200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:120553600-120556200	Active TSS	Esophagus	oesophagus
12	chr12:120553600-120556200	Active TSS	Lung	lung
13	chr12:120553600-120556200	Active TSS	GM12878-XiMat	blood
14	chr12:120553600-120556200	Active TSS	NHLF	lung
15	chr12:120553600-120556600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:120553800-120555600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:120553800-120555800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:120553800-120555800	Active TSS	Left Ventricle	heart
19	chr12:120553800-120556000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:120553800-120556000	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:120553800-120556000	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr12:120553800-120556000	Active TSS	Small Intestine	intestine
23	chr12:120553800-120556000	Active TSS	NHDF-Ad	bronchial
24	chr12:120553800-120556200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:120553800-120556200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:120553800-120556200	Active TSS	Psoas Muscle	Psoas
27	chr12:120553800-120556200	Active TSS	Right Ventricle	heart
28	chr12:120553800-120556400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr12:120553800-120556400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:120553800-120556400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:120553800-120556800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr12:120554000-120555600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:120554000-120555600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:120554000-120555600	Active TSS	Brain Anterior Caudate	brain
35	chr12:120554000-120555600	Active TSS	Colon Smooth Muscle	Colon
36	chr12:120554000-120555600	Active TSS	Fetal Intestine Small	intestine
37	chr12:120554000-120555600	Active TSS	Placenta Amnion	Placenta Amnion
38	chr12:120554000-120555600	Active TSS	Spleen	Spleen
39	chr12:120554000-120555600	Active TSS	NH-A	brain
40	chr12:120554000-120555800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:120554000-120555800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:120554000-120555800	Active TSS	Muscle Satellite Cultured Cells	--
43	chr12:120554000-120555800	Active TSS	Brain Hippocampus Middle	brain
44	chr12:120554000-120555800	Active TSS	Fetal Intestine Large	intestine
45	chr12:120554000-120555800	Active TSS	Fetal Lung	lung
46	chr12:120554000-120555800	Active TSS	K562	blood
47	chr12:120554000-120556000	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr12:120554000-120556000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr12:120554000-120556000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:120554000-120556000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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