Variant report

Variant	rs12227259
Chromosome Location	chr12:29670504-29670505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:29670442-29670568	GM12878	blood:	n/a	n/a
2	CTCF	chr12:29670460-29670610	RPTEC	kidney:	n/a	n/a
3	RAD21	chr12:29670269-29670667	ECC-1	luminal epithelium:	n/a	n/a
4	RAD21	chr12:29670348-29670552	K562	blood:	n/a	n/a
5	CTCF	chr12:29670394-29670576	MCF-7	breast:	n/a	n/a
6	CTCF	chr12:29670360-29670510	RPTEC	kidney:	n/a	n/a
7	CTCF	chr12:29670420-29670570	HEEpiC	esophagus:	n/a	n/a
8	CTCF	chr12:29670400-29670550	MCF-7	breast:	n/a	n/a
9	CTCF	chr12:29670408-29670515	MCF-7	breast:	n/a	n/a
10	CEBPB	chr12:29670127-29670523	K562	blood:	n/a	chr12:29670253-29670270
11	CEBPB	chr12:29670243-29670644	MCF-7	breast:	n/a	chr12:29670549-29670562 chr12:29670253-29670270
12	CTCF	chr12:29670404-29670602	Pancreas_OC	pancreas:	n/a	n/a
13	CTCF	chr12:29670440-29670590	GM12871	blood:	n/a	n/a
14	CTCF	chr12:29670420-29670570	Caco-2	colon:	n/a	n/a
15	RAD21	chr12:29670126-29670700	HCT-116	colon:	n/a	n/a
16	CTCF	chr12:29670440-29670590	SAEC	small airway:	n/a	n/a
17	RAD21	chr12:29670314-29670621	A549	lung:	n/a	n/a
18	RAD21	chr12:29670386-29670590	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr12:29670300-29670615	HepG2	liver:	n/a	n/a
20	CTCF	chr12:29670460-29670610	MCF-7	breast:	n/a	n/a
21	CTCF	chr12:29670406-29670576	Hela-S3	cervix:	n/a	n/a
22	RAD21	chr12:29670342-29670583	SK-N-SH_RA	brain:	n/a	n/a
23	CEBPB	chr12:29670215-29670622	MCF-7	breast:	n/a	chr12:29670549-29670562 chr12:29670253-29670270
24	CTCF	chr12:29670440-29670590	GM06990	blood:	n/a	n/a
25	SMC3	chr12:29670210-29670666	Hela-S3	cervix:	n/a	n/a
26	ATF1	chr12:29670347-29670556	K562	blood:	n/a	n/a
27	CTCF	chr12:29670440-29670590	HEEpiC	esophagus:	n/a	n/a
28	CTCF	chr12:29670396-29670608	LNCaP	prostate:	n/a	n/a
29	CTCF	chr12:29670401-29670533	MCF-7	breast:	n/a	n/a
30	CTCF	chr12:29670360-29670510	WERI-Rb-1	eye:	n/a	n/a
31	CTCF	chr12:29670411-29670585	LNCaP	prostate:	n/a	n/a
32	CTCF	chr12:29670420-29670570	WERI-Rb-1	eye:	n/a	n/a
33	RAD21	chr12:29670341-29670591	MCF-7	breast:	n/a	n/a
34	CTCF	chr12:29670433-29670579	GM10248	blood:	n/a	n/a
35	RAD21	chr12:29670372-29670580	GM12878	blood:	n/a	n/a
36	RAD21	chr12:29670286-29670595	SK-N-SH_RA	brain:	n/a	n/a
37	SMC3	chr12:29670349-29670641	HepG2	liver:	n/a	n/a
38	CTCF	chr12:29670145-29670667	HCT-116	colon:	n/a	n/a
39	RAD21	chr12:29670282-29670627	MCF-7	breast:	n/a	n/a
40	CTCF	chr12:29670413-29670514	GM12892	blood:	n/a	n/a
41	CTCF	chr12:29670316-29670673	K562	blood:	n/a	n/a
42	CTCF	chr12:29670314-29670572	T-47D	breast:	n/a	n/a
43	CTCF	chr12:29670400-29670550	Caco-2	colon:	n/a	n/a
44	CTCF	chr12:29670247-29670736	MCF-7	breast:	n/a	n/a
45	CTCF	chr12:29670414-29670539	Gliobla	brain:	n/a	n/a
46	CTCF	chr12:29670272-29670755	MCF-7	breast:	n/a	n/a
47	CTCF	chr12:29670388-29670595	K562	blood:	n/a	n/a
48	CEBPB	chr12:29669466-29670641	Hela-S3	cervix:	n/a	chr12:29670549-29670562 chr12:29670253-29670270
49	CTCF	chr12:29670420-29670570	BE2_C	brain:	n/a	n/a
50	RAD21	chr12:29670193-29670687	HCT-116	colon:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:29670448..29671322-chr6:3936086..3937016,2	MCF-7	breast:
2	chr12:29462346..29462982-chr12:29670343..29670928,2	K562	blood:
3	chr12:29669971..29670947-chr12:30997067..30997929,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257456	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11050264	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050265	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12164837	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319420	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29600600-29675600	Weak transcription	Psoas Muscle	Psoas
2	chr12:29650400-29699000	Weak transcription	Right Ventricle	heart
3	chr12:29652200-29673200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:29653400-29672200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:29655400-29672200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:29656200-29673800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:29657200-29675600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:29658000-29680200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:29658000-29681200	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:29658400-29690200	Weak transcription	HMEC	breast
11	chr12:29658600-29678800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:29660000-29672800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:29660800-29690000	Weak transcription	NHDF-Ad	bronchial
14	chr12:29663400-29671600	Strong transcription	Left Ventricle	heart
15	chr12:29664000-29671600	Strong transcription	Adipose Nuclei	Adipose
16	chr12:29664000-29671600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:29665800-29675000	Weak transcription	Fetal Heart	heart
19	chr12:29666000-29671000	Weak transcription	Esophagus	oesophagus
20	chr12:29666600-29671600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:29666800-29670600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:29666800-29670600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:29666800-29671000	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:29667000-29671600	Strong transcription	Fetal Stomach	stomach
25	chr12:29667000-29680200	Weak transcription	Fetal Kidney	kidney
26	chr12:29667200-29672000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:29667200-29695600	Weak transcription	Ovary	ovary
28	chr12:29668600-29674600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:29668600-29690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:29668600-29695800	Weak transcription	Aorta	Aorta
31	chr12:29668800-29706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:29669000-29670600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:29669200-29671000	Strong transcription	Spleen	Spleen
35	chr12:29669200-29671200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:29669200-29671600	Strong transcription	Hela-S3	cervix
37	chr12:29669800-29670600	Genic enhancers	HSMM	muscle
38	chr12:29669800-29672600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:29669800-29673600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:29670000-29670600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:29670000-29671200	Weak transcription	Brain Angular Gyrus	brain
42	chr12:29670000-29672600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:29670000-29673400	Weak transcription	Brain Anterior Caudate	brain
44	chr12:29670000-29674000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:29670000-29674000	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr12:29670200-29670600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:29670200-29670600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:29670400-29670600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:29670400-29670800	Enhancers	Fetal Brain Male	brain

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