Variant report

Variant	rs28478308
Chromosome Location	chr12:124017569-124017570
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	MAX	chr12:124017255-124019286	HepG2	liver:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
2	POLR2A	chr12:124017557-124019155	K562	blood:	n/a	n/a
3	POLR2A	chr12:124017306-124019150	HepG2	liver:	n/a	n/a
4	TBL1XR1	chr12:124017265-124017940	K562	blood:	n/a	n/a
5	CBX3	chr12:124017259-124018108	K562	blood:	n/a	n/a
6	ZNF143	chr12:124017292-124017846	K562	blood:	n/a	n/a
7	MAX	chr12:124017326-124019119	K562	blood:	n/a	chr12:124017624-124017639
8	SIN3AK20	chr12:124017519-124017799	K562	blood:	n/a	n/a
9	ELF1	chr12:124017480-124017784	HepG2	liver:	n/a	chr12:124017651-124017664
10	CEBPB	chr12:124017334-124018091	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr12:124017387-124018114	HepG2	liver:	n/a	chr12:124017624-124017639
12	ZNF143	chr12:124017375-124017974	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:124017562-124019144	HUVEC	blood vessel:	n/a	n/a
14	MAX	chr12:124017269-124019274	A549	lung:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
15	REST	chr12:124017537-124018039	A549	lung:	n/a	n/a
16	CREB1	chr12:124017473-124018163	A549	lung:	n/a	n/a
17	CHD2	chr12:124017413-124018001	K562	blood:	n/a	n/a
18	ELF1	chr12:124017437-124017831	HepG2	liver:	n/a	chr12:124017651-124017664
19	TBL1XR1	chr12:124017312-124017633	K562	blood:	n/a	n/a
20	TAF1	chr12:124017566-124018105	HepG2	liver:	n/a	n/a
21	MYC	chr12:124017455-124018127	MCF10A-Er-Src	breast:	n/a	chr12:124017624-124017639
22	RCOR1	chr12:124016551-124018022	K562	blood:	n/a	n/a
23	ZMIZ1	chr12:124017276-124018020	K562	blood:	n/a	n/a
24	GABPA	chr12:124017543-124017917	K562	blood:	n/a	chr12:124017630-124017639
25	BRCA1	chr12:124017418-124017970	Hela-S3	cervix:	n/a	n/a
26	MAX	chr12:124017459-124018605	Hela-S3	cervix:	n/a	chr12:124017624-124017639
27	POLR2A	chr12:124017559-124018108	H1-hESC	embryonic stem cell:	n/a	n/a
28	E2F6	chr12:124017363-124018308	H1-hESC	embryonic stem cell:	n/a	n/a
29	MXI1	chr12:124017442-124017673	K562	blood:	n/a	n/a
30	MAZ	chr12:124016579-124019401	IMR90	lung:	n/a	chr12:124019137-124019147 chr12:124016824-124016835 chr12:124017249-124017259 chr12:124017624-124017639
31	NR2F2	chr12:124016531-124018094	K562	blood:	n/a	n/a
32	MAX	chr12:124017303-124018190	H1-hESC	embryonic stem cell:	n/a	chr12:124017624-124017639
33	ELF1	chr12:124017362-124017936	K562	blood:	n/a	chr12:124017651-124017664
34	E2F6	chr12:124017502-124018246	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr12:124017425-124018291	H1-hESC	embryonic stem cell:	n/a	chr12:124017624-124017639
36	SIN3AK20	chr12:124017544-124018197	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr12:124017515-124019142	A549	lung:	n/a	n/a
38	CREB1	chr12:124017568-124018148	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYC	chr12:124016769-124019025	K562	blood:	n/a	chr12:124016824-124016835 chr12:124017249-124017259 chr12:124017624-124017639
40	MXI1	chr12:124017183-124019192	IMR90	lung:	n/a	n/a
41	TAF1	chr12:124017492-124018872	HepG2	liver:	n/a	n/a
42	MYC	chr12:124017262-124019228	A549	lung:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
43	TEAD4	chr12:124017337-124018107	K562	blood:	n/a	n/a
44	MAZ	chr12:124017507-124019189	K562	blood:	n/a	chr12:124019137-124019147 chr12:124017624-124017639
45	ARID3A	chr12:124017367-124017624	K562	blood:	n/a	n/a
46	E2F6	chr12:124017443-124018183	A549	lung:	n/a	n/a
47	SIN3A	chr12:124017433-124018093	H1-hESC	embryonic stem cell:	n/a	n/a
48	HMGN3	chr12:124017509-124019090	K562	blood:	n/a	n/a
49	TBP	chr12:124017444-124018088	K562	blood:	n/a	n/a
50	E2F6	chr12:124017474-124018601	K562	blood:	n/a	chr12:124018461-124018468 chr12:124018312-124018321 chr12:124018465-124018475 chr12:124018468-124018478

No.	Distal block	Cell Line	Cell type
1	chr12:123997284..124000079-chr12:124017073..124019484,2	MCF-7	breast:
2	chr12:124015709..124018064-chr12:124066858..124069100,3	MCF-7	breast:
3	chr12:123947470..123950375-chr12:124015636..124018854,3	K562	blood:
4	chr12:123872416..123876102-chr12:124017252..124019601,4	MCF-7	breast:
5	chr12:124006455..124008310-chr12:124016022..124017705,2	K562	blood:
6	chr12:123871385..123875741-chr12:124017374..124019532,6	MCF-7	breast:
7	chr12:123753293..123757508-chr12:124015727..124020202,5	K562	blood:
8	chr12:124015786..124020200-chr12:124020787..124024805,6	K562	blood:
9	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
10	chr12:124016749..124018606-chr12:124069216..124071514,2	K562	blood:
11	chr12:123948940..123951509-chr12:124017235..124019368,2	MCF-7	breast:
12	chr12:123998884..124001416-chr12:124016546..124018370,2	K562	blood:
13	chr12:123943032..123944561-chr12:124016969..124018583,2	MCF-7	breast:
14	chr12:124017444..124019100-chr12:124084646..124086674,2	MCF-7	breast:

Variant related genes	Relation type
MIR3908	TF binding region
ENSG00000183955	Chromatin interaction
ENSG00000266655	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1057879	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11522338	0.81[AMR][1000 genomes]
rs11522339	0.81[AMR][1000 genomes]
rs2048615	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2333831	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28371124	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28430750	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28450070	0.81[AMR][1000 genomes]
rs28478446	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28497190	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28535055	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28580741	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28605072	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28701527	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28707421	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28712858	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28741988	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv13410	chr12:124017022-124017617	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv3357232	chr12:124017349-124019447	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 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	chr12:124006200-124017600	Weak transcription	Small Intestine	intestine
2	chr12:124015400-124018000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr12:124016000-124017600	Flanking Active TSS	Brain Substantia Nigra	brain
4	chr12:124016200-124017800	Flanking Active TSS	HUVEC	blood vessel
5	chr12:124016200-124018000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:124016400-124017600	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:124016400-124017600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:124016400-124017600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:124016400-124017600	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr12:124016400-124017600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
11	chr12:124016400-124017600	Bivalent Enhancer	Fetal Thymus	thymus
12	chr12:124016400-124017600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr12:124016400-124017600	Enhancers	Spleen	Spleen
14	chr12:124016400-124017600	Flanking Active TSS	Osteobl	bone
15	chr12:124016400-124018000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr12:124016400-124018000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:124016400-124018000	Flanking Active TSS	HMEC	breast
18	chr12:124016400-124019400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:124016600-124017600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:124016600-124017600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:124016600-124017600	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr12:124016600-124017800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:124016600-124017800	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr12:124016600-124017800	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:124016600-124017800	Flanking Active TSS	HepG2	liver
26	chr12:124016600-124017800	Flanking Active TSS	NH-A	brain
27	chr12:124016600-124018000	Flanking Active TSS	Placenta	Placenta
28	chr12:124016800-124017600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:124016800-124017600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr12:124016800-124017600	Enhancers	Stomach Mucosa	stomach
31	chr12:124016800-124017600	Flanking Active TSS	NHEK	skin
32	chr12:124016800-124017800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr12:124016800-124017800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr12:124016800-124017800	Flanking Active TSS	Fetal Heart	heart
35	chr12:124016800-124017800	Flanking Active TSS	K562	blood
36	chr12:124016800-124018000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
37	chr12:124016800-124018000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:124016800-124019000	Active TSS	Left Ventricle	heart
39	chr12:124016800-124019200	Active TSS	Aorta	Aorta
40	chr12:124016800-124019400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:124016800-124019400	Active TSS	Right Atrium	heart
42	chr12:124017000-124017800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr12:124017000-124018000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr12:124017000-124018000	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr12:124017000-124018000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:124017000-124018000	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr12:124017000-124018200	Flanking Active TSS	Dnd41	blood
48	chr12:124017000-124019000	Active TSS	NHDF-Ad	bronchial
49	chr12:124017000-124019200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:124017000-124019200	Active TSS	Ovary	ovary

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