Variant report

Variant	rs28421797
Chromosome Location	chr12:124016764-124016765
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	SPI1	chr12:124016561-124017124	HL-60	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
2	MYC	chr12:124016700-124016938	HUVEC	blood vessel:	n/a	chr12:124016824-124016835
3	MTA3	chr12:124016504-124017129	GM12878	blood:	n/a	n/a
4	IRF4	chr12:124016529-124017044	GM12878	blood:	n/a	n/a
5	MAX	chr12:124016594-124017026	K562	blood:	n/a	chr12:124016824-124016835
6	POLR2A	chr12:124016415-124017057	HUVEC	blood vessel:	n/a	n/a
7	SPI1	chr12:124016727-124016899	K562	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
8	RCOR1	chr12:124016551-124018022	K562	blood:	n/a	n/a
9	SPI1	chr12:124016654-124017059	HL-60	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
10	RCOR1	chr12:124016717-124016826	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr12:124016579-124019401	IMR90	lung:	n/a	chr12:124019137-124019147 chr12:124016824-124016835 chr12:124017249-124017259 chr12:124017624-124017639
12	NR2F2	chr12:124016531-124018094	K562	blood:	n/a	n/a
13	POLR2A	chr12:124016548-124017056	HL-60	blood:	n/a	n/a
14	RUNX3	chr12:124016461-124017071	GM12878	blood:	n/a	n/a
15	NFIC	chr12:124016615-124017037	GM12878	blood:	n/a	n/a
16	RUNX3	chr12:124016450-124017068	GM12878	blood:	n/a	n/a
17	NFIC	chr12:124016616-124017030	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:124016739-124017152	PFSK-1	brain:	n/a	n/a
19	SPI1	chr12:124016545-124017032	GM12891	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
20	SPI1	chr12:124016613-124017008	GM12878	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
21	WRNIP1	chr12:124016511-124016933	GM12878	blood:	n/a	n/a
22	SPI1	chr12:124016301-124017227	GM12878	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
23	EP300	chr12:124016661-124016963	GM12878	blood:	n/a	chr12:124016839-124016848 chr12:124016835-124016849
24	SPI1	chr12:124016730-124016949	GM12878	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
25	RCOR1	chr12:124016450-124016789	K562	blood:	n/a	n/a
26	EBF1	chr12:124016665-124016903	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:124016649-124017156	HUVEC	blood vessel:	n/a	n/a
28	BCL11A	chr12:124016656-124016943	GM12878	blood:	n/a	chr12:124016835-124016844
29	RCOR1	chr12:124016438-124018290	IMR90	lung:	n/a	n/a
30	BCLAF1	chr12:124016596-124017027	GM12878	blood:	n/a	chr12:124016835-124016844
31	SPI1	chr12:124016564-124017053	GM12891	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
32	MXI1	chr12:124016550-124019478	SK-N-SH	brain:	n/a	n/a
33	ZNF143	chr12:124016291-124016930	K562	blood:	n/a	n/a
34	POLR2A	chr12:124016595-124017050	HL-60	blood:	n/a	n/a
35	REST	chr12:124016691-124016958	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr12:124014798-124016776	K562	blood:	n/a	n/a
37	POLR2A	chr12:124016589-124016929	HUVEC	blood vessel:	n/a	n/a
38	MAX	chr12:124016614-124016974	NB4	blood:	n/a	chr12:124016824-124016835
39	POLR2A	chr12:124016405-124016771	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123955912..123957787-chr12:124014886..124016796,2	K562	blood:
2	chr12:124015709..124018064-chr12:124066858..124069100,3	MCF-7	breast:
3	chr12:123947470..123950375-chr12:124015636..124018854,3	K562	blood:
4	chr12:124006455..124008310-chr12:124016022..124017705,2	K562	blood:
5	chr12:123753293..123757508-chr12:124015727..124020202,5	K562	blood:
6	chr12:124015786..124020200-chr12:124020787..124024805,6	K562	blood:
7	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
8	chr12:124016749..124018606-chr12:124069216..124071514,2	K562	blood:
9	chr12:123873494..123875550-chr12:124015653..124017169,2	MCF-7	breast:
10	chr12:123998884..124001416-chr12:124016546..124018370,2	K562	blood:

Variant related genes	Relation type
MIR3908	TF binding region
ENSG00000111328	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000266655	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs34224739	1.00[ASN][1000 genomes]
rs34506612	1.00[ASN][1000 genomes]
rs34705855	1.00[ASN][1000 genomes]
rs55920625	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' 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	45 gene(s)	inside rSNPs	diseases
6	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv560495	chr12:124012974-124017461	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124001200-124017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:124001400-124017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:124002000-124016800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:124004600-124016800	Weak transcription	Stomach Mucosa	stomach
5	chr12:124006200-124017600	Weak transcription	Small Intestine	intestine
6	chr12:124006800-124016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:124007800-124017000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:124007800-124017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:124008000-124017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:124008000-124017400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:124008200-124017200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:124008400-124017400	Weak transcription	Gastric	stomach
13	chr12:124014400-124016800	Genic enhancers	Fetal Heart	heart
14	chr12:124015000-124016800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:124015000-124016800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:124015200-124017000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:124015200-124017200	Genic enhancers	Fetal Stomach	stomach
18	chr12:124015200-124017400	Enhancers	Pancreas	Pancrea
19	chr12:124015400-124017000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:124015400-124018000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr12:124015600-124016800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
22	chr12:124015800-124016800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr12:124015800-124016800	Enhancers	Ovary	ovary
24	chr12:124015800-124017000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:124015800-124017200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:124015800-124017200	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr12:124015800-124017400	Enhancers	Esophagus	oesophagus
28	chr12:124016000-124016800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:124016000-124017400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr12:124016000-124017400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr12:124016000-124017400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:124016000-124017400	Enhancers	Fetal Lung	lung
33	chr12:124016000-124017600	Flanking Active TSS	Brain Substantia Nigra	brain
34	chr12:124016200-124016800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:124016200-124016800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr12:124016200-124016800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:124016200-124017000	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:124016200-124017200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:124016200-124017400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:124016200-124017800	Flanking Active TSS	HUVEC	blood vessel
41	chr12:124016200-124018000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr12:124016400-124016800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:124016400-124016800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:124016400-124016800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:124016400-124016800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
46	chr12:124016400-124016800	Flanking Active TSS	Right Atrium	heart
47	chr12:124016400-124016800	Enhancers	GM12878-XiMat	blood
48	chr12:124016400-124016800	Transcr. at gene 5' and 3'	HSMM	muscle
49	chr12:124016400-124016800	Transcr. at gene 5' and 3'	NHEK	skin
50	chr12:124016400-124017000	Flanking Active TSS	Right Ventricle	heart

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