Variant report

Variant	rs12712978
Chromosome Location	chr2:47078320-47078321
allele	G/T
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	EP300	chr2:47073928-47078551	SK-N-SH	brain:	n/a	chr2:47077523-47077533 chr2:47076132-47076146 chr2:47077719-47077726
2	TEAD4	chr2:47077827-47078358	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr2:47077685-47078425	ECC-1	luminal epithelium:	n/a	chr2:47077719-47077726
4	NFIC	chr2:47077668-47078466	ECC-1	luminal epithelium:	n/a	n/a
5	TEAD4	chr2:47076816-47078460	SK-N-SH	brain:	n/a	n/a
6	MAX	chr2:47077767-47078426	SK-N-SH	brain:	n/a	chr2:47078067-47078076
7	EP300	chr2:47071015-47078457	SK-N-SH	brain:	n/a	chr2:47077523-47077533 chr2:47076132-47076146 chr2:47077719-47077726
8	RCOR1	chr2:47073664-47078554	IMR90	lung:	n/a	n/a
9	FOSL2	chr2:47077724-47078449	SK-N-SH	brain:	n/a	chr2:47078139-47078148 chr2:47078064-47078075 chr2:47078068-47078076
10	PBX3	chr2:47077752-47078390	SK-N-SH	brain:	n/a	chr2:47078138-47078147
11	MAZ	chr2:47076242-47078509	IMR90	lung:	n/a	chr2:47077671-47077681 chr2:47078067-47078076
12	GATA3	chr2:47075931-47078483	A549	lung:	n/a	chr2:47077022-47077029 chr2:47077022-47077029 chr2:47077015-47077036 chr2:47077017-47077033 chr2:47077022-47077029 chr2:47076130-47076141 chr2:47077020-47077030 chr2:47076208-47076218
13	TEAD4	chr2:47076157-47078405	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr2:47076105-47078515	SK-N-SH	brain:	n/a	chr2:47077022-47077029 chr2:47077022-47077029 chr2:47077015-47077036 chr2:47077017-47077033 chr2:47077022-47077029 chr2:47076130-47076141 chr2:47077020-47077030 chr2:47076208-47076218
15	POLR2A	chr2:47077748-47078326	HUVEC	blood vessel:	n/a	n/a
16	TCF12	chr2:47077666-47078493	ECC-1	luminal epithelium:	n/a	n/a
17	MAX	chr2:47077072-47078392	HCT-116	colon:	n/a	chr2:47077671-47077681 chr2:47078067-47078076
18	NFIC	chr2:47077836-47078334	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr2:47076721-47078656	A549	lung:	n/a	chr2:47077671-47077681 chr2:47078067-47078076
20	MXI1	chr2:47073719-47078370	IMR90	lung:	n/a	n/a
21	TCF12	chr2:47073594-47078762	A549	lung:	n/a	chr2:47075434-47075444
22	TCF12	chr2:47073279-47078605	SK-N-SH	brain:	n/a	chr2:47075434-47075444
23	TCF12	chr2:47077798-47078417	ECC-1	luminal epithelium:	n/a	n/a
24	TCF7L2	chr2:47078172-47078351	PANC-1	pancreas:	n/a	chr2:47078246-47078253
25	REST	chr2:47077800-47078338	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr2:47074290-47078661	IMR90	lung:	n/a	n/a
27	MAX	chr2:47076794-47078457	SK-N-SH	brain:	n/a	chr2:47077671-47077681 chr2:47078067-47078076
28	TCF12	chr2:47075910-47078535	SK-N-SH	brain:	n/a	n/a
29	PBX3	chr2:47076713-47078438	SK-N-SH	brain:	n/a	chr2:47078138-47078147
30	MAX	chr2:47075764-47078736	A549	lung:	n/a	chr2:47077671-47077681 chr2:47078067-47078076
31	FOSL2	chr2:47077729-47078437	A549	lung:	n/a	chr2:47078139-47078148 chr2:47078064-47078075 chr2:47078068-47078076
32	FOSL1	chr2:47077638-47078344	HCT-116	colon:	n/a	chr2:47078139-47078148 chr2:47078064-47078075 chr2:47078068-47078076
33	POLR2A	chr2:47076047-47078345	SK-N-SH	brain:	n/a	n/a
34	NFIC	chr2:47077754-47078430	SK-N-SH	brain:	n/a	n/a
35	NFIC	chr2:47073728-47078587	SK-N-SH	brain:	n/a	chr2:47076448-47076465 chr2:47074602-47074619 chr2:47076449-47076465

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47072263..47075274-chr2:47076219..47078746,3	K562	blood:
2	chr2:47077957..47080077-chr2:47082546..47084432,2	K562	blood:

Variant related genes	Relation type
LINC01119	TF binding region
ENSG00000239332	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11125097	0.83[AMR][1000 genomes];0.88[EUR][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47069400-47082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:47072000-47078400	Enhancers	Lung	lung
3	chr2:47072000-47078400	Enhancers	Right Ventricle	heart
4	chr2:47072000-47078600	Enhancers	Fetal Stomach	stomach
5	chr2:47072000-47078600	Enhancers	Ovary	ovary
6	chr2:47072200-47078400	Enhancers	Left Ventricle	heart
7	chr2:47072200-47078600	Enhancers	Pancreas	Pancrea
8	chr2:47072200-47078800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr2:47072400-47078600	Enhancers	Fetal Intestine Small	intestine
10	chr2:47072600-47078400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:47072600-47078400	Enhancers	Fetal Heart	heart
12	chr2:47072600-47078800	Enhancers	HUVEC	blood vessel
13	chr2:47072600-47080400	Enhancers	HMEC	breast
14	chr2:47072800-47078600	Enhancers	Right Atrium	heart
15	chr2:47072800-47078600	Enhancers	NHDF-Ad	bronchial
16	chr2:47072800-47080200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:47072800-47080400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:47073400-47078600	Enhancers	Stomach Mucosa	stomach
19	chr2:47073400-47078600	Enhancers	Osteobl	bone
20	chr2:47073600-47078600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:47073600-47078800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:47073800-47078400	Enhancers	Psoas Muscle	Psoas
23	chr2:47073800-47078400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr2:47073800-47078600	Enhancers	NHEK	skin
25	chr2:47074000-47078600	Enhancers	HSMM	muscle
26	chr2:47074000-47079600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:47075000-47078600	Enhancers	Gastric	stomach
28	chr2:47075200-47080400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:47075200-47084400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:47075400-47078800	Enhancers	Hela-S3	cervix
31	chr2:47076000-47078400	Enhancers	Colonic Mucosa	Colon
32	chr2:47076000-47078600	Enhancers	Fetal Muscle Trunk	muscle
33	chr2:47076600-47081600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:47076800-47081600	Weak transcription	Brain Anterior Caudate	brain
35	chr2:47077000-47078400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr2:47077000-47078600	Enhancers	Fetal Muscle Leg	muscle
37	chr2:47077000-47080600	Enhancers	K562	blood
38	chr2:47077200-47078400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:47077200-47078600	Enhancers	Colon Smooth Muscle	Colon
40	chr2:47077200-47079800	Enhancers	Rectal Smooth Muscle	rectum
41	chr2:47077200-47086200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:47077400-47081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:47077600-47078400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr2:47077600-47078400	Enhancers	HSMMtube	muscle
45	chr2:47077600-47081600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:47077600-47081600	Weak transcription	Brain Hippocampus Middle	brain
47	chr2:47077600-47081600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:47077800-47079600	Enhancers	Placenta	Placenta
49	chr2:47078000-47078600	Enhancers	NHLF	lung
50	chr2:47078000-47079200	Enhancers	Skeletal Muscle Male	skeletal muscle

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