Variant report

Variant	rs28384802
Chromosome Location	chr12:1739614-1739615
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	CTCF	chr12:1739520-1739670	HRPEpiC	eye:	n/a	chr12:1739583-1739596
2	SUZ12	chr12:1739328-1740832	NT2-D1	testis:	n/a	n/a
3	CTCF	chr12:1739607-1739761	GM13977	blood:	n/a	n/a
4	CTCF	chr12:1739580-1739730	AG09309	skin:	n/a	chr12:1739583-1739596
5	CTCF	chr12:1739597-1739757	GM19238	blood:	n/a	n/a
6	CTCF	chr12:1739600-1739750	GM12866	blood:	n/a	n/a
7	CTCF	chr12:1739601-1739782	ProgFib	skin:	n/a	n/a
8	CTCF	chr12:1739520-1739670	GM12872	blood:	n/a	chr12:1739583-1739596
9	CTCF	chr12:1739560-1739710	HCFaa	heart:	n/a	chr12:1739583-1739596
10	CTCF	chr12:1739603-1739743	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr12:1739604-1739766	GM19240	blood:	n/a	n/a
12	CTCF	chr12:1739520-1739670	GM12874	blood:	n/a	chr12:1739583-1739596
13	CTCF	chr12:1739602-1739723	Lung_OC	lung:	n/a	n/a
14	MAX	chr12:1739001-1739628	NB4	blood:	n/a	chr12:1739003-1739013 chr12:1739601-1739611
15	CTCF	chr12:1738798-1740032	SK-N-SH	brain:	n/a	chr12:1739583-1739596 chr12:1739411-1739424 chr12:1739311-1739324 chr12:1739309-1739327 chr12:1739247-1739265 chr12:1739121-1739134 chr12:1739119-1739137
16	CTCF	chr12:1739560-1739710	SAEC	small airway:	n/a	chr12:1739583-1739596
17	E2F6	chr12:1739384-1739983	A549	lung:	n/a	chr12:1739417-1739426
18	MAX	chr12:1739023-1740020	A549	lung:	n/a	chr12:1739601-1739611
19	NFIC	chr12:1739346-1739939	ECC-1	luminal epithelium:	n/a	n/a
20	CTCF	chr12:1739600-1739750	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chr12:1738969-1739867	GM12878	blood:	n/a	chr12:1739583-1739596 chr12:1739411-1739424 chr12:1739311-1739324 chr12:1739309-1739327 chr12:1739247-1739265 chr12:1739121-1739134 chr12:1739119-1739137
22	MAX	chr12:1739579-1739644	Hela-S3	cervix:	n/a	chr12:1739601-1739611
23	CTCF	chr12:1739014-1739843	MCF-7	breast:	n/a	chr12:1739583-1739596 chr12:1739411-1739424 chr12:1739311-1739324 chr12:1739309-1739327 chr12:1739247-1739265 chr12:1739121-1739134 chr12:1739119-1739137
24	CTCF	chr12:1739500-1739650	HRPEpiC	eye:	n/a	chr12:1739583-1739596
25	MAX	chr12:1739518-1740284	H1-hESC	embryonic stem cell:	n/a	chr12:1740060-1740069 chr12:1740059-1740066 chr12:1740058-1740067 chr12:1739601-1739611
26	CTCF	chr12:1739558-1739821	MCF-7	breast:	n/a	chr12:1739583-1739596
27	CTCF	chr12:1739570-1739798	MCF-7	breast:	n/a	chr12:1739583-1739596
28	MAX	chr12:1739425-1740006	A549	lung:	n/a	chr12:1739601-1739611
29	CTCF	chr12:1739580-1739730	HPF	lung:	n/a	chr12:1739583-1739596
30	CTCF	chr12:1739580-1739730	NHEK	skin:	n/a	chr12:1739583-1739596
31	CTCF	chr12:1739600-1739750	HPF	lung:	n/a	n/a
32	ZBTB7A	chr12:1738857-1739984	ECC-1	luminal epithelium:	n/a	chr12:1739440-1739448 chr12:1739416-1739425 chr12:1738964-1738978
33	CTCF	chr12:1739580-1739730	AG10803	skin:	n/a	chr12:1739583-1739596
34	CTCF	chr12:1739600-1739750	WERI-Rb-1	eye:	n/a	n/a
35	MAX	chr12:1739417-1739930	MCF-7	breast:	n/a	chr12:1739601-1739611
36	CTCF	chr12:1739600-1739750	HEEpiC	esophagus:	n/a	n/a
37	CTCF	chr12:1739580-1739870	AG04450	lung:	n/a	chr12:1739583-1739596
38	CTCF	chr12:1739586-1739808	NHEK	skin:	n/a	n/a
39	CTCF	chr12:1739580-1739818	GM12892	blood:	n/a	chr12:1739583-1739596
40	CTCF	chr12:1739540-1739690	HUVEC	blood vessel:	n/a	chr12:1739583-1739596
41	CTCF	chr12:1739540-1739690	HEEpiC	esophagus:	n/a	chr12:1739583-1739596
42	POLR2A	chr12:1739555-1739681	GM12878	blood:	n/a	n/a
43	CTCF	chr12:1739591-1739794	MCF-7	breast:	n/a	n/a
44	CTCF	chr12:1739580-1739730	SK-N-SH_RA	brain:	n/a	chr12:1739583-1739596
45	EBF1	chr12:1739532-1739836	GM12878	blood:	n/a	n/a
46	CTCF	chr12:1739268-1739725	IMR90	lung:	n/a	chr12:1739583-1739596 chr12:1739411-1739424 chr12:1739311-1739324 chr12:1739309-1739327
47	CTCF	chr12:1739600-1739750	SAEC	small airway:	n/a	n/a
48	TCF7L2	chr12:1738414-1739817	HCT-116	colon:	n/a	chr12:1739110-1739124 chr12:1739109-1739125 chr12:1739113-1739122 chr12:1739109-1739125 chr12:1738615-1738625 chr12:1738617-1738626
49	ZBTB7A	chr12:1738734-1740013	ECC-1	luminal epithelium:	n/a	chr12:1739440-1739448 chr12:1739416-1739425 chr12:1738964-1738978
50	EP300	chr12:1737662-1740910	SK-N-SH	brain:	n/a	chr12:1740199-1740213 chr12:1739522-1739538 chr12:1739309-1739318

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1714212..1714749-chr12:1739345..1739945,2	MCF-7	breast:
2	chr12:1703157..1705505-chr12:1739226..1741204,2	MCF-7	breast:

Variant related genes	Relation type
WNT5B	TF binding region
ENSG00000171823	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10773971	0.84[ASN][1000 genomes]
rs11061881	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270034	0.92[EUR][1000 genomes]
rs7966046	0.86[ASN][1000 genomes]
rs886848	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv898587	chr12:1732295-1756642	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv898588	chr12:1736314-1755960	Bivalent Enhancer Enhancers Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv556994	chr12:1737309-1743843	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv898589	chr12:1738111-1755654	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 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	chr12:1733000-1744000	Weak transcription	K562	blood
2	chr12:1737600-1740600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:1737800-1739800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:1737800-1740000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:1737800-1740400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr12:1737800-1740600	Enhancers	Spleen	Spleen
7	chr12:1737800-1740800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr12:1737800-1740800	Bivalent Enhancer	Fetal Lung	lung
9	chr12:1738000-1740000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:1738000-1740000	Enhancers	Fetal Brain Male	brain
11	chr12:1738000-1740000	Enhancers	Fetal Heart	heart
12	chr12:1738200-1740200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
13	chr12:1738200-1740400	Active TSS	Rectal Smooth Muscle	rectum
14	chr12:1738400-1739800	Flanking Active TSS	Pancreas	Pancrea
15	chr12:1738400-1740000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
16	chr12:1738400-1740400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:1738400-1740600	Enhancers	Lung	lung
18	chr12:1738600-1739800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:1738600-1739800	Flanking Active TSS	Liver	Liver
20	chr12:1738600-1739800	Active TSS	Brain Angular Gyrus	brain
21	chr12:1738600-1739800	Active TSS	Brain Anterior Caudate	brain
22	chr12:1738600-1739800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:1738600-1739800	Active TSS	Fetal Brain Female	brain
24	chr12:1738600-1739800	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr12:1738600-1740000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:1738600-1740000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr12:1738600-1740000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:1738600-1740000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:1738600-1740000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:1738600-1740000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:1738600-1740200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:1738600-1740200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr12:1738600-1740200	Flanking Active TSS	Right Ventricle	heart
34	chr12:1738600-1740400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr12:1738600-1740600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:1738600-1740600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:1738600-1740600	Active TSS	Colon Smooth Muscle	Colon
38	chr12:1738600-1740800	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr12:1738800-1739800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:1738800-1739800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:1738800-1739800	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr12:1738800-1739800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr12:1738800-1739800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:1738800-1739800	Active TSS	Brain Hippocampus Middle	brain
45	chr12:1738800-1739800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:1738800-1739800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr12:1738800-1740000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr12:1738800-1740000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:1738800-1740000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr12:1738800-1740000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin

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