Variant report

Variant	rs559385862
Chromosome Location	chr12:42984652-42984653
allele	A/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	CTCF	chr12:42984500-42984689	MCF-7	breast:	n/a	chr12:42984591-42984609
2	NR2F2	chr12:42984229-42984882	MCF-7	breast:	n/a	n/a
3	CTCF	chr12:42984512-42984684	H1-hESC	embryonic stem cell:	n/a	chr12:42984591-42984609
4	CTCF	chr12:42984520-42984670	HRE	kidney:	n/a	chr12:42984591-42984609
5	CTBP2	chr12:42982768-42984725	H1-hESC	embryonic stem cell:	n/a	n/a
6	SP1	chr12:42984075-42984749	A549	lung:	n/a	chr12:42984232-42984241
7	MXI1	chr12:42982100-42984824	IMR90	lung:	n/a	chr12:42984253-42984268
8	CTCF	chr12:42984520-42984670	MCF-7	breast:	n/a	chr12:42984591-42984609
9	EP300	chr12:42982235-42984855	ECC-1	luminal epithelium:	n/a	chr12:42982351-42982361 chr12:42983501-42983510 chr12:42983498-42983507 chr12:42984759-42984773
10	CTCF	chr12:42984520-42984670	HMEC	breast:	n/a	chr12:42984591-42984609
11	CTCF	chr12:42984511-42984686	MCF-7	breast:	n/a	chr12:42984591-42984609
12	RAD21	chr12:42984288-42984786	H1-hESC	embryonic stem cell:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
13	CTCF	chr12:42984520-42984670	HRPEpiC	eye:	n/a	chr12:42984591-42984609
14	NFIC	chr12:42982719-42984696	ECC-1	luminal epithelium:	n/a	n/a
15	RAD21	chr12:42984339-42984828	ECC-1	luminal epithelium:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
16	POLR2A	chr12:42983191-42984783	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr12:42984520-42984670	AG09309	skin:	n/a	chr12:42984591-42984609
18	RAD21	chr12:42984344-42984799	SK-N-SH_RA	brain:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
19	RAD21	chr12:42983993-42984818	ECC-1	luminal epithelium:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
20	CTCF	chr12:42984509-42984702	NHEK	skin:	n/a	chr12:42984591-42984609
21	CTCF	chr12:42984620-42984770	BE2_C	brain:	n/a	n/a
22	TEAD4	chr12:42983012-42984809	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr12:42984520-42984670	RPTEC	kidney:	n/a	chr12:42984591-42984609
24	RAD21	chr12:42984436-42984748	SK-N-SH_RA	brain:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
25	CTCF	chr12:42984538-42984656	Gliobla	brain:	n/a	chr12:42984591-42984609
26	MAZ	chr12:42981376-42985082	IMR90	lung:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
27	CTCF	chr12:42984536-42984675	MCF-7	breast:	n/a	chr12:42984591-42984609
28	CTCF	chr12:42984536-42984676	GM19238	blood:	n/a	chr12:42984591-42984609
29	MAX	chr12:42982660-42984847	ECC-1	luminal epithelium:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
30	CTCF	chr12:42984540-42984690	AoAF	blood vessel:	n/a	chr12:42984591-42984609
31	CTCF	chr12:42984540-42984681	Fibrobl	skin:	n/a	chr12:42984591-42984609
32	TCF12	chr12:42983986-42984953	ECC-1	luminal epithelium:	n/a	n/a
33	CTCF	chr12:42984533-42984677	A549	lung:	n/a	chr12:42984591-42984609
34	SMC3	chr12:42982437-42984934	SK-N-SH	brain:	n/a	chr12:42982812-42982819 chr12:42984593-42984607 chr12:42982868-42982882
35	CTCF	chr12:42984526-42984672	MCF-7	breast:	n/a	chr12:42984591-42984609
36	CTCF	chr12:42984522-42984677	MCF-7	breast:	n/a	chr12:42984591-42984609
37	SP1	chr12:42984039-42984669	A549	lung:	n/a	chr12:42984232-42984241
38	RAD21	chr12:42981077-42985218	SK-N-SH	brain:	n/a	chr12:42983223-42983235 chr12:42982867-42982886 chr12:42984597-42984607 chr12:42984597-42984609
39	TAF1	chr12:42982944-42984815	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr12:42983361-42984689	MCF10A-Er-Src	breast:	n/a	n/a
41	MAX	chr12:42982586-42984897	ECC-1	luminal epithelium:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
42	CTCF	chr12:42984408-42984725	K562	blood:	n/a	chr12:42984591-42984609
43	MXI1	chr12:42980685-42985161	SK-N-SH	brain:	n/a	chr12:42984253-42984268
44	CTCF	chr12:42984520-42984670	HPAF	blood vessel:	n/a	chr12:42984591-42984609
45	CTCF	chr12:42984580-42984730	AG04449	skin:	n/a	chr12:42984591-42984609
46	RAD21	chr12:42983860-42984800	H1-hESC	embryonic stem cell:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
47	ZBTB7A	chr12:42982586-42984766	ECC-1	luminal epithelium:	n/a	n/a
48	RAD21	chr12:42984340-42984799	H1-hESC	embryonic stem cell:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
49	CTCF	chr12:42984620-42984770	HepG2	liver:	n/a	n/a
50	MAX	chr12:42982680-42984684	A549	lung:	n/a	chr12:42983670-42983679 chr12:42984534-42984544

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42984197..42984716-chr12:43676086..43676642,2	MCF-7	breast:

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv989438	chr12:42981066-42988699	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3361465	chr12:42982310-42984858	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3339962	chr12:42982685-42984683	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42980000-42985000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:42981200-42985000	Active TSS	Right Atrium	heart
3	chr12:42981400-42984800	Active TSS	Right Ventricle	heart
4	chr12:42981600-42985000	Active TSS	Fetal Kidney	kidney
5	chr12:42981800-42984800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr12:42982000-42984800	Active TSS	Aorta	Aorta
7	chr12:42982000-42984800	Active TSS	Left Ventricle	heart
8	chr12:42982000-42984800	Active TSS	Ovary	ovary
9	chr12:42982000-42985000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:42982400-42984800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:42982400-42984800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:42982400-42984800	Active TSS	Psoas Muscle	Psoas
13	chr12:42982600-42984800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr12:42982600-42984800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:42983200-42984800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:42983600-42984800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:42983800-42984800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr12:42984000-42984800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
19	chr12:42984000-42984800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:42984000-42984800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:42984000-42984800	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr12:42984000-42984800	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr12:42984000-42984800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
24	chr12:42984000-42984800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
25	chr12:42984000-42984800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
26	chr12:42984000-42984800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
27	chr12:42984000-42984800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr12:42984000-42984800	Flanking Active TSS	HSMM	muscle
29	chr12:42984000-42985000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr12:42984000-42985000	Flanking Active TSS	HUVEC	blood vessel
31	chr12:42984200-42984800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
32	chr12:42984200-42984800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:42984200-42984800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
34	chr12:42984200-42984800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:42984200-42984800	Bivalent Enhancer	Small Intestine	intestine
36	chr12:42984200-42984800	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr12:42984200-42984800	Flanking Active TSS	HSMMtube	muscle
38	chr12:42984200-42984800	Flanking Bivalent TSS/Enh	NHEK	skin
39	chr12:42984200-42985000	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr12:42984200-42985000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
41	chr12:42984200-42985000	Flanking Bivalent TSS/Enh	Osteobl	bone
42	chr12:42984400-42984800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:42984400-42984800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr12:42984400-42984800	Bivalent Enhancer	Placenta	Placenta
45	chr12:42984400-42984800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
46	chr12:42984400-42984800	Enhancers	Spleen	Spleen
47	chr12:42984400-42985000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
48	chr12:42984400-42985000	Bivalent Enhancer	Fetal Brain Male	brain
49	chr12:42984400-42985200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
50	chr12:42984400-42987200	Weak transcription	Gastric	stomach

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