Variant report

Variant	rs28405771
Chromosome Location	chr12:121976176-121976177
allele	A/C
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	chr12:121973624-121976489	SK-N-SH	brain:	n/a	n/a
2	PML	chr12:121975889-121976721	GM12878	blood:	n/a	n/a
3	ZNF143	chr12:121975957-121976836	GM12878	blood:	n/a	chr12:121976005-121976015 chr12:121976059-121976077
4	SMARCB1	chr12:121973841-121976449	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr12:121976165-121976557	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:121976040-121976914	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:121973653-121976782	GM19193	blood:	n/a	n/a
8	MTA3	chr12:121975829-121977061	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:121973609-121976415	GM18951	blood:	n/a	n/a
10	POLR2A	chr12:121974590-121976343	NB4	blood:	n/a	n/a
11	MAZ	chr12:121973768-121976444	GM12878	blood:	n/a	chr12:121975043-121975053 chr12:121974080-121974090 chr12:121976078-121976088
12	POLR2A	chr12:121973761-121976612	GM12892	blood:	n/a	n/a
13	MAX	chr12:121973713-121977024	ECC-1	luminal epithelium:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121974080-121974090 chr12:121976078-121976088 chr12:121973741-121973751
14	YY1	chr12:121974887-121976404	GM12878	blood:	n/a	chr12:121975615-121975629 chr12:121975132-121975143 chr12:121975973-121975987 chr12:121975824-121975833 chr12:121975520-121975531 chr12:121975822-121975833 chr12:121976161-121976172 chr12:121975821-121975830 chr12:121975528-121975542 chr12:121975522-121975536 chr12:121976080-121976089
15	POLR2A	chr12:121973711-121976427	GM12892	blood:	n/a	n/a
16	POLR2A	chr12:121973296-121976832	GM12878	blood:	n/a	n/a
17	SPI1	chr12:121976150-121976614	HL-60	blood:	n/a	chr12:121976159-121976172
18	POLR2A	chr12:121974854-121976257	ECC-1	luminal epithelium:	n/a	n/a
19	REST	chr12:121973568-121976423	H1-neurons	neurons:	n/a	chr12:121973990-121974003 chr12:121975043-121975056 chr12:121976004-121976014 chr12:121974811-121974821 chr12:121974313-121974333
20	SIN3A	chr12:121973896-121976198	H1-hESC	embryonic stem cell:	n/a	chr12:121976005-121976014 chr12:121973948-121973958 chr12:121975763-121975776
21	POLR2A	chr12:121973451-121976845	GM12878	blood:	n/a	n/a
22	HA-E2F1	chr12:121974740-121976786	MCF-7	breast:	n/a	chr12:121975949-121975959 chr12:121975822-121975832 chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975738-121975750 chr12:121975528-121975537 chr12:121976110-121976120
23	MTA3	chr12:121976121-121976601	GM12878	blood:	n/a	n/a
24	RUNX3	chr12:121972246-121977055	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:121975798-121976256	H1-neurons	neurons:	n/a	n/a
26	MYC	chr12:121974465-121976545	NB4	blood:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121976078-121976088
27	YY1	chr12:121975913-121976469	GM12878	blood:	n/a	chr12:121975973-121975987 chr12:121976161-121976172 chr12:121976080-121976089
28	MAX	chr12:121974423-121976422	HepG2	liver:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121976078-121976088
29	HA-E2F1	chr12:121974897-121976285	Hela-S3	cervix:	n/a	chr12:121975949-121975959 chr12:121975822-121975832 chr12:121975551-121975565 chr12:121975135-121975147 chr12:121975738-121975750 chr12:121975528-121975537 chr12:121976110-121976120
30	POLR2A	chr12:121973935-121976698	GM18526	blood:	n/a	n/a
31	SPI1	chr12:121976145-121976573	GM12891	blood:	n/a	chr12:121976159-121976172
32	MAX	chr12:121974534-121976241	Hela-S3	cervix:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121976078-121976088
33	MXI1	chr12:121973532-121976787	IMR90	lung:	n/a	n/a
34	POLR2A	chr12:121976003-121976457	GM12878	blood:	n/a	n/a
35	MAX	chr12:121974450-121976192	MCF-7	breast:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121976078-121976088
36	STAT1	chr12:121976152-121976346	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:121973596-121976536	GM18505	blood:	n/a	n/a
38	ELF1	chr12:121974578-121976533	GM12878	blood:	n/a	chr12:121975821-121975830 chr12:121975824-121975833 chr12:121975526-121975538 chr12:121975106-121975118 chr12:121975822-121975834 chr12:121975222-121975233
39	ESRRA	chr12:121973467-121976969	GM12878	blood:	n/a	chr12:121974785-121974795 chr12:121974923-121974932 chr12:121976855-121976865 chr12:121976855-121976865 chr12:121976853-121976869 chr12:121976853-121976865 chr12:121975088-121975101
40	MAX	chr12:121976157-121977017	ECC-1	luminal epithelium:	n/a	n/a
41	ZKSCAN1	chr12:121976158-121976323	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:121973953-121976406	GM15510	blood:	n/a	n/a
43	POLR2A	chr12:121973581-121976880	Raji	blood:	n/a	n/a
44	TAF1	chr12:121974474-121976190	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr12:121973919-121976773	GM19099	blood:	n/a	n/a
46	POLR2A	chr12:121973637-121976561	HL-60	blood:	n/a	n/a
47	PAX5	chr12:121974726-121976250	GM12892	blood:	n/a	n/a
48	POLR2A	chr12:121975838-121976215	HUVEC	blood vessel:	n/a	n/a
49	RUNX3	chr12:121976139-121977084	GM12878	blood:	n/a	n/a
50	STAT5A	chr12:121975886-121976580	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121973453..121977492-chr12:122016919..122020388,4	K562	blood:
2	chr12:121974674..121977649-chr12:122063134..122066400,4	MCF-7	breast:
3	chr12:121974857..121978322-chr12:122063131..122066228,6	MCF-7	breast:
4	chr12:121974542..121976684-chr12:122017365..122019196,2	MCF-7	breast:
5	chr12:121966142..121973158-chr12:121973289..121976781,9	MCF-7	breast:
6	chr12:121973525..121977245-chr12:122063799..122066216,4	K562	blood:
7	chr12:121975167..121976771-chr12:122063978..122066637,2	K562	blood:
8	chr12:121974972..121977558-chr12:122231894..122235040,4	MCF-7	breast:
9	chr12:121937924..121939615-chr12:121975554..121978350,2	MCF-7	breast:
10	chr12:121945860..121947775-chr12:121975322..121977515,3	MCF-7	breast:
11	chr12:121974472..121977117-chr12:122150068..122152069,2	MCF-7	breast:
12	chr12:121972742..121976523-chr12:121985100..121990052,4	K562	blood:
13	chr12:121973342..121977941-chr12:121987524..121992877,7	MCF-7	breast:
14	chr12:121974810..121976577-chr12:122237441..122239422,3	MCF-7	breast:
15	chr12:121975126..121978118-chr12:121985924..121988501,3	MCF-7	breast:

Variant related genes	Relation type
KDM2B	TF binding region
ENSG00000188735	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000182500	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1617736	1.00[CEU][hapmap]
rs28625063	0.80[ASN][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	nsv560457	chr12:121956483-121976176	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
4	esv3354947	chr12:121974194-121976742	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121973200-121976800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:121973400-121976800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:121973600-121976400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:121973600-121976400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:121973600-121976600	Flanking Active TSS	Colonic Mucosa	Colon
6	chr12:121973600-121976600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:121973600-121976800	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr12:121973800-121976400	Flanking Active TSS	NH-A	brain
9	chr12:121973800-121976600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr12:121973800-121976800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:121974000-121976200	Active TSS	Aorta	Aorta
12	chr12:121974000-121976200	Active TSS	Brain Anterior Caudate	brain
13	chr12:121974000-121976200	Active TSS	Colon Smooth Muscle	Colon
14	chr12:121974000-121976200	Active TSS	Fetal Brain Female	brain
15	chr12:121974000-121976200	Active TSS	Ovary	ovary
16	chr12:121974000-121976200	Active TSS	Psoas Muscle	Psoas
17	chr12:121974000-121976200	Active TSS	Rectal Smooth Muscle	rectum
18	chr12:121974000-121976400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:121974000-121976400	Active TSS	Right Atrium	heart
20	chr12:121974000-121976600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:121974000-121976600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:121974200-121976400	Active TSS	Left Ventricle	heart
23	chr12:121974200-121976400	Weak transcription	Dnd41	blood
24	chr12:121974200-121976600	Active TSS	Right Ventricle	heart
25	chr12:121974400-121976200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:121974400-121976200	Active TSS	Brain Angular Gyrus	brain
27	chr12:121974400-121976400	Active TSS	Brain Substantia Nigra	brain
28	chr12:121974400-121976800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr12:121974600-121976200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:121974600-121976200	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:121974600-121976400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:121974600-121976400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:121974600-121976400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:121974600-121976400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:121974600-121976800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr12:121974800-121976200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr12:121974800-121976200	Active TSS	Brain Hippocampus Middle	brain
38	chr12:121974800-121976200	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr12:121974800-121976200	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr12:121974800-121976200	Active TSS	Lung	lung
41	chr12:121974800-121976200	Active TSS	Small Intestine	intestine
42	chr12:121974800-121976200	Active TSS	Stomach Mucosa	stomach
43	chr12:121974800-121976200	Active TSS	Hela-S3	cervix
44	chr12:121974800-121976400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr12:121974800-121976400	Active TSS	Gastric	stomach
46	chr12:121975000-121976200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:121975000-121976200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:121975000-121976200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:121975000-121976200	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr12:121975000-121976200	Active TSS	HUES64 Cell Line	embryonic stem cell

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