Variant report

Variant	rs3741863
Chromosome Location	chr12:63327947-63327948
allele	C/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	HDAC2	chr12:63327942-63328259	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZEB1	chr12:63326895-63329453	HepG2	liver:	n/a	chr12:63329095-63329107 chr12:63329096-63329107
3	UBTF	chr12:63327632-63329147	K562	blood:	n/a	n/a
4	MAX	chr12:63327017-63329477	A549	lung:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
5	HA-E2F1	chr12:63326823-63329443	MCF-7	breast:	n/a	chr12:63327280-63327287 chr12:63328820-63328835 chr12:63328824-63328836 chr12:63328892-63328902 chr12:63328827-63328836 chr12:63328554-63328563
6	POLR2A	chr12:63327070-63328289	K562	blood:	n/a	n/a
7	EGR1	chr12:63327568-63328249	K562	blood:	n/a	chr12:63327868-63327881 chr12:63327868-63327881 chr12:63327870-63327880 chr12:63327868-63327881 chr12:63327868-63327882 chr12:63327864-63327886 chr12:63327870-63327880 chr12:63327871-63327880 chr12:63327869-63327880
8	RAD21	chr12:63327902-63328589	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr12:63327940-63328090	GM12866	blood:	n/a	n/a
10	CTCF	chr12:63327880-63328030	GM06990	blood:	n/a	n/a
11	MAZ	chr12:63327643-63329318	K562	blood:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
12	REST	chr12:63327942-63329046	HL-60	blood:	n/a	chr12:63328186-63328204 chr12:63328536-63328549 chr12:63328229-63328242
13	CTCF	chr12:63327840-63327990	MCF-7	breast:	n/a	n/a
14	MAX	chr12:63327821-63328602	ECC-1	luminal epithelium:	n/a	chr12:63328552-63328562 chr12:63327895-63327905
15	EP300	chr12:63327681-63329383	ECC-1	luminal epithelium:	n/a	chr12:63328524-63328540 chr12:63328836-63328852 chr12:63329304-63329314 chr12:63327741-63327755 chr12:63328246-63328255 chr12:63328558-63328567
16	MAX	chr12:63327672-63329329	K562	blood:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
17	CHD1	chr12:63327829-63327958	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr12:63327924-63329494	HCT-116	colon:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63328924-63328933
19	POLR2A	chr12:63327689-63329320	MCF-7	breast:	n/a	n/a
20	MAX	chr12:63327826-63329295	K562	blood:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
21	CTCF	chr12:63327749-63329511	A549	lung:	n/a	chr12:63328666-63328679 chr12:63328545-63328558 chr12:63328548-63328561
22	SIN3A	chr12:63326943-63329353	H1-hESC	embryonic stem cell:	n/a	chr12:63328666-63328677
23	TCF12	chr12:63327895-63329441	A549	lung:	n/a	n/a
24	BHLHE40	chr12:63326926-63329361	K562	blood:	n/a	chr12:63328948-63328964 chr12:63328794-63328810 chr12:63328667-63328683 chr12:63328526-63328542 chr12:63328523-63328539 chr12:63328885-63328901
25	MYC	chr12:63327623-63329348	K562	blood:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
26	MAX	chr12:63326953-63329378	MCF-7	breast:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
27	TAF1	chr12:63327884-63329240	ECC-1	luminal epithelium:	n/a	n/a
28	SIN3AK20	chr12:63327763-63329519	MCF-7	breast:	n/a	n/a
29	ELF1	chr12:63327882-63329338	MCF-7	breast:	n/a	chr12:63328706-63328718 chr12:63328558-63328570
30	E2F4	chr12:63327854-63329297	K562	blood:	n/a	chr12:63328820-63328835 chr12:63328824-63328836 chr12:63328892-63328902 chr12:63328827-63328836 chr12:63328554-63328563
31	RCOR1	chr12:63326883-63329350	K562	blood:	n/a	n/a
32	MYC	chr12:63327752-63329257	NB4	blood:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
33	KAP1	chr12:63326884-63328347	HEK293	kidney:	n/a	n/a
34	POLR2A	chr12:63327604-63329140	K562	blood:	n/a	n/a
35	MYC	chr12:63327589-63329314	K562	blood:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
36	RAD21	chr12:63327670-63328593	MCF-7	breast:	n/a	n/a
37	POLR2A	chr12:63327662-63329197	K562	blood:	n/a	n/a
38	REST	chr12:63327817-63329501	H1-neurons	neurons:	n/a	chr12:63328186-63328204 chr12:63328536-63328549 chr12:63328229-63328242
39	HMGN3	chr12:63327775-63329218	K562	blood:	n/a	n/a
40	CTCF	chr12:63327893-63328469	MCF-7	breast:	n/a	n/a
41	EGR1	chr12:63327655-63328121	K562	blood:	n/a	chr12:63327868-63327881 chr12:63327868-63327881 chr12:63327870-63327880 chr12:63327868-63327881 chr12:63327868-63327882 chr12:63327864-63327886 chr12:63327870-63327880 chr12:63327871-63327880 chr12:63327869-63327880
42	UBTF	chr12:63327533-63329210	K562	blood:	n/a	n/a
43	TCF12	chr12:63327936-63329451	ECC-1	luminal epithelium:	n/a	n/a
44	NR2F2	chr12:63327904-63329435	MCF-7	breast:	n/a	n/a
45	MAX	chr12:63327874-63329420	A549	lung:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
46	POLR2A	chr12:63327873-63329170	HL-60	blood:	n/a	n/a
47	ZBTB7A	chr12:63327757-63329365	ECC-1	luminal epithelium:	n/a	chr12:63328597-63328608 chr12:63329072-63329081
48	POLR2A	chr12:63327682-63329206	K562	blood:	n/a	n/a
49	MAX	chr12:63327660-63329325	ECC-1	luminal epithelium:	n/a	chr12:63328681-63328691 chr12:63328552-63328562 chr12:63327895-63327905 chr12:63328924-63328933
50	HDAC2	chr12:63326945-63329435	MCF-7	breast:	n/a	chr12:63329372-63329386

No.	Distal block	Cell Line	Cell type
1	chr12:62995343..62997102-chr12:63326865..63328948,2	K562	blood:
2	chr12:63325863..63329962-chr12:63356030..63360907,6	MCF-7	breast:
3	chr12:63327630..63329589-chr12:63447421..63451204,3	MCF-7	breast:
4	chr12:62996812..62998536-chr12:63327281..63329321,2	MCF-7	breast:
5	chr12:63244647..63247922-chr12:63326690..63328475,3	MCF-7	breast:
6	chr12:63326223..63329085-chr20:52208224..52210688,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252660	TF binding region
PPM1H	TF binding region
ENSG00000257354	Chromatin interaction
ENSG00000257664	Chromatin interaction
ENSG00000139239	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000199179	Chromatin interaction
ENSG00000200296	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11174725	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12230183	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4763042	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61920303	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61920305	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs699589	1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7295848	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv899162	chr12:63279750-63334242	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv3355722	chr12:63327210-63330258	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv3378901	chr12:63327535-63330133	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63326400-63329200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:63326400-63329400	Active TSS	Brain Angular Gyrus	brain
3	chr12:63326600-63328200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:63326600-63329200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:63326600-63330000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:63326800-63328000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:63326800-63328200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:63326800-63328200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr12:63326800-63328200	Flanking Active TSS	Liver	Liver
10	chr12:63326800-63328200	Active TSS	Right Atrium	heart
11	chr12:63326800-63328400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr12:63326800-63328600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr12:63326800-63329000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:63326800-63329400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr12:63326800-63329400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr12:63326800-63329400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:63326800-63329400	Active TSS	Psoas Muscle	Psoas
18	chr12:63326800-63329400	Active TSS	Right Ventricle	heart
19	chr12:63326800-63329400	Active TSS	Stomach Mucosa	stomach
20	chr12:63326800-63329600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr12:63327000-63328000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:63327000-63328000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:63327000-63328000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr12:63327000-63328200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr12:63327000-63328200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
26	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
28	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr12:63327000-63328200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr12:63327000-63328400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr12:63327000-63328400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
32	chr12:63327000-63328600	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr12:63327000-63329000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:63327000-63329000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr12:63327000-63329200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr12:63327000-63329200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr12:63327000-63329200	Active TSS	Aorta	Aorta
38	chr12:63327000-63329200	Active TSS	Brain Anterior Caudate	brain
39	chr12:63327000-63329200	Active TSS	Osteobl	bone
40	chr12:63327000-63329400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:63327000-63329400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:63327000-63329400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:63327000-63329400	Active TSS	Gastric	stomach
44	chr12:63327000-63329400	Active TSS	Left Ventricle	heart
45	chr12:63327000-63329600	Active TSS	Brain Hippocampus Middle	brain
46	chr12:63327000-63329600	Active TSS	Fetal Kidney	kidney
47	chr12:63327200-63328000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr12:63327200-63328000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
49	chr12:63327200-63328000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
50	chr12:63327200-63328000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood

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