Variant report

Variant	rs12306866
Chromosome Location	chr12:49737114-49737115
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	CTBP2	chr12:49735158-49737394	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr12:49736312-49737428	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOS	chr12:49737091-49737242	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr12:49736759-49737518	K562	blood:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
5	NR2F2	chr12:49736039-49737343	K562	blood:	n/a	n/a
6	MAZ	chr12:49736995-49737300	K562	blood:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
7	RCOR1	chr12:49736996-49737277	K562	blood:	n/a	n/a
8	STAT5A	chr12:49737052-49737308	GM12878	blood:	n/a	n/a
9	EGR1	chr12:49737014-49737502	K562	blood:	n/a	chr12:49737409-49737422
10	MAX	chr12:49736162-49737386	A549	lung:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
11	MAX	chr12:49737040-49737371	K562	blood:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
12	BHLHE40	chr12:49736173-49737372	K562	blood:	n/a	n/a
13	POLR2A	chr12:49737096-49737504	H1-neurons	neurons:	n/a	n/a
14	MYC	chr12:49737023-49737337	K562	blood:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
15	SIN3AK20	chr12:49737087-49737543	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZBTB7A	chr12:49735808-49737533	ECC-1	luminal epithelium:	n/a	chr12:49736374-49736383 chr12:49736793-49736801
17	MAX	chr12:49736017-49737563	ECC-1	luminal epithelium:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
18	CTCF	chr12:49737080-49737230	K562	blood:	n/a	n/a
19	CTCF	chr12:49735821-49737540	A549	lung:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736885-49736898 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
20	ZBTB7A	chr12:49735973-49737145	ECC-1	luminal epithelium:	n/a	chr12:49736374-49736383 chr12:49736793-49736801
21	MAX	chr12:49735989-49737509	A549	lung:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
22	CTCF	chr12:49737091-49737293	GM19238	blood:	n/a	n/a
23	BHLHE40	chr12:49737053-49737276	GM12878	blood:	n/a	n/a
24	PBX3	chr12:49737039-49737219	GM12878	blood:	n/a	n/a
25	KAP1	chr12:49736041-49737458	U2OS	brain:	n/a	n/a
26	HDAC2	chr12:49736934-49737421	K562	blood:	n/a	n/a
27	RCOR1	chr12:49736973-49737350	K562	blood:	n/a	n/a
28	CTCF	chr12:49736980-49737130	GM12864	blood:	n/a	n/a
29	CTCF	chr12:49737080-49737230	GM12867	blood:	n/a	n/a
30	MYC	chr12:49737022-49737338	K562	blood:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
31	KAP1	chr12:49735830-49737382	HEK293	kidney:	n/a	n/a
32	MAX	chr12:49737111-49737368	K562	blood:	n/a	chr12:49737195-49737202 chr12:49737194-49737203 chr12:49737192-49737207 chr12:49737185-49737201
33	CTCF	chr12:49737060-49737210	GM12878	blood:	n/a	n/a
34	SIN3AK20	chr12:49737083-49737368	A549	lung:	n/a	n/a
35	PBX3	chr12:49735911-49737424	SK-N-SH	brain:	n/a	n/a
36	NR2F2	chr12:49736942-49737316	K562	blood:	n/a	n/a
37	BACH1	chr12:49736346-49737145	H1-hESC	embryonic stem cell:	n/a	n/a
38	BCL3	chr12:49736967-49737381	GM12878	blood:	n/a	n/a
39	TCF12	chr12:49735879-49737500	ECC-1	luminal epithelium:	n/a	chr12:49737328-49737335
40	SIN3A	chr12:49735631-49737614	H1-hESC	embryonic stem cell:	n/a	chr12:49737000-49737013 chr12:49737455-49737463 chr12:49735808-49735821

No.	Distal block	Cell Line	Cell type
1	chr12:49734512..49737434-chr12:49761201..49764804,3	K562	blood:
2	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
3	chr12:49709675..49711213-chr12:49736436..49739309,2	MCF-7	breast:
4	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
5	chr12:49668999..49670991-chr12:49736933..49738497,2	K562	blood:
6	chr12:49725155..49726080-chr12:49735903..49737150,6	MCF-7	breast:
7	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
8	chr12:49725123..49726098-chr12:49735996..49737262,7	K562	blood:
9	chr12:49685452..49688091-chr12:49734714..49737225,2	MCF-7	breast:
10	chr12:49662709..49665978-chr12:49735321..49738677,4	K562	blood:
11	chr12:49735114..49738057-chr12:49759505..49762701,3	K562	blood:
12	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
13	chr12:49661766..49665978-chr12:49735321..49738677,5	K562	blood:

Variant related genes	Relation type
DNAJC22	TF binding region
ENSG00000135406	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10400435	0.82[CHB][hapmap]
rs10506284	1.00[JPT][hapmap]
rs10506285	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11168975	0.82[CHB][hapmap]
rs11168981	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169016	1.00[JPT][hapmap]
rs11169058	1.00[JPT][hapmap]
rs11169059	1.00[JPT][hapmap]
rs11831313	0.88[ASN][1000 genomes]
rs11834161	1.00[JPT][hapmap]
rs11835071	0.82[ASN][1000 genomes]
rs11835303	0.82[CHB][hapmap]
rs12296440	1.00[JPT][hapmap]
rs12299777	0.94[ASN][1000 genomes]
rs12301632	1.00[JPT][hapmap]
rs12305716	1.00[JPT][hapmap]
rs12306118	1.00[JPT][hapmap]
rs12309053	1.00[JPT][hapmap]
rs12310129	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12315996	1.00[JPT][hapmap]
rs12317856	0.88[ASN][1000 genomes]
rs12322561	1.00[JPT][hapmap]
rs12580931	0.82[CHB][hapmap]
rs12822293	0.82[CHB][hapmap]
rs17123696	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1874909	0.94[ASN][1000 genomes]
rs1874910	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1874911	0.94[ASN][1000 genomes]
rs2270741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2272478	1.00[JPT][hapmap]
rs3088008	0.82[CHB][hapmap]
rs4243545	0.82[CHB][hapmap]
rs4898519	0.82[CHB][hapmap]
rs60331259	0.88[ASN][1000 genomes]
rs60494978	0.88[ASN][1000 genomes]
rs6580707	1.00[JPT][hapmap]
rs6580709	1.00[JPT][hapmap]
rs6580716	1.00[JPT][hapmap]
rs7139061	1.00[JPT][hapmap]
rs7294648	1.00[JPT][hapmap]
rs7294973	1.00[JPT][hapmap]
rs7295162	1.00[JPT][hapmap]
rs7309997	1.00[JPT][hapmap]
rs7342365	1.00[JPT][hapmap]
rs74089059	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74089062	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7955245	0.88[ASN][1000 genomes]
rs7955541	1.00[JPT][hapmap]
rs7962951	1.00[JPT][hapmap]
rs7969099	1.00[JPT][hapmap]
rs7976165	1.00[JPT][hapmap]
rs9919740	1.00[JPT][hapmap]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49734200-49739400	Weak transcription	Hela-S3	cervix
2	chr12:49735400-49737200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:49735600-49737400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
6	chr12:49735800-49737200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:49735800-49737200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
8	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
9	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
10	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:49735800-49737400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
12	chr12:49735800-49737800	Enhancers	Gastric	stomach
13	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
14	chr12:49736000-49737200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:49736000-49737200	Flanking Bivalent TSS/Enh	NH-A	brain
19	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:49736000-49737400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
25	chr12:49736000-49737400	Enhancers	Lung	lung
26	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
27	chr12:49736000-49737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
28	chr12:49736000-49737600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
29	chr12:49736000-49737800	Enhancers	Pancreas	Pancrea
30	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
31	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
33	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
35	chr12:49736200-49737200	Bivalent Enhancer	HMEC	breast
36	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	NHEK	skin
37	chr12:49736200-49737200	Flanking Bivalent TSS/Enh	Osteobl	bone
38	chr12:49736200-49737400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
39	chr12:49736200-49737400	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
40	chr12:49736200-49737400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
41	chr12:49736200-49737800	Bivalent Enhancer	Fetal Thymus	thymus
42	chr12:49736400-49737200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:49736400-49737200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr12:49736400-49737200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr12:49736400-49737400	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr12:49736400-49737400	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr12:49736400-49737600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
48	chr12:49736400-49737600	Bivalent Enhancer	Placenta	Placenta
49	chr12:49736400-49738000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
50	chr12:49736600-49737200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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