Variant report

Variant	rs7980628
Chromosome Location	chr12:118569347-118569348
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	MXI1	chr12:118569293-118570247	HepG2	liver:	n/a	n/a
2	NFIC	chr12:118569165-118570311	HepG2	liver:	n/a	chr12:118569438-118569455 chr12:118569924-118569940 chr12:118569924-118569941 chr12:118569438-118569454
3	MYBL2	chr12:118569142-118570329	HepG2	liver:	n/a	n/a
4	NFIC	chr12:118569180-118570265	ECC-1	luminal epithelium:	n/a	chr12:118569438-118569455 chr12:118569924-118569940 chr12:118569924-118569941 chr12:118569438-118569454
5	TEAD4	chr12:118569169-118569617	HepG2	liver:	n/a	n/a
6	TBP	chr12:118569235-118569585	HepG2	liver:	n/a	n/a
7	ARID3A	chr12:118569244-118569505	HepG2	liver:	n/a	n/a
8	MBD4	chr12:118569243-118569582	HepG2	liver:	n/a	n/a
9	TEAD4	chr12:118569260-118570184	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr12:118569262-118569654	HepG2	liver:	n/a	chr12:118569438-118569455 chr12:118569438-118569454
11	POLR2A	chr12:118569324-118569630	HepG2	liver:	n/a	n/a
12	HEY1	chr12:118569224-118569620	HepG2	liver:	n/a	n/a
13	MAX	chr12:118569232-118569602	ECC-1	luminal epithelium:	n/a	n/a
14	EP300	chr12:118569188-118569568	HepG2	liver:	n/a	chr12:118569341-118569355 chr12:118569342-118569356
15	EP300	chr12:118569256-118570179	ECC-1	luminal epithelium:	n/a	chr12:118569341-118569355 chr12:118569342-118569356
16	POLR2A	chr12:118569294-118569659	HepG2	liver:	n/a	n/a
17	NFIC	chr12:118569195-118570185	ECC-1	luminal epithelium:	n/a	chr12:118569438-118569455 chr12:118569924-118569940 chr12:118569924-118569941 chr12:118569438-118569454
18	POLR2A	chr12:118569274-118569630	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:118567809..118570427-chr12:118572115..118574740,3	MCF-7	breast:
2	chr12:118568705..118570458-chr12:118572215..118574320,2	K562	blood:
3	chr12:118558694..118561471-chr12:118568462..118574858,6	MCF-7	breast:

Variant related genes	Relation type
PEBP1	TF binding region
ENSG00000089220	Chromatin interaction
ENSG00000176834	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10850961	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1092854	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11068826	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs11068830	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151901	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs11830698	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1277175	0.80[CHB][hapmap]
rs2088702	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2249624	0.85[JPT][hapmap]
rs353887	0.85[JPT][hapmap]
rs353896	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs364823	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs3847650	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3847651	0.80[CHB][hapmap]
rs3927167	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3956808	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs404566	0.85[JPT][hapmap]
rs418941	0.84[JPT][hapmap]
rs4590911	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767664	0.85[JPT][hapmap]
rs575121	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs6490167	0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6490168	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71450262	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7314781	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs795482	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7976200	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978165	0.95[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118542400-118569400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:118542600-118569400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:118542600-118572800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:118542600-118573400	Weak transcription	Primary T cells from cord blood	blood
5	chr12:118545400-118569600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:118546400-118569400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:118552800-118572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:118552800-118573400	Weak transcription	Aorta	Aorta
9	chr12:118553000-118573000	Weak transcription	Fetal Brain Female	brain
10	chr12:118558800-118572800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:118559200-118569400	Weak transcription	Adipose Nuclei	Adipose
12	chr12:118559200-118569400	Weak transcription	Dnd41	blood
13	chr12:118559200-118569600	Weak transcription	GM12878-XiMat	blood
14	chr12:118559200-118569800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:118559200-118570000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:118559200-118572600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:118559200-118572600	Weak transcription	NHEK	skin
18	chr12:118559200-118572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:118559200-118573000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:118559200-118573000	Weak transcription	Fetal Kidney	kidney
21	chr12:118559200-118573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:118559200-118573400	Weak transcription	Fetal Intestine Small	intestine
23	chr12:118559400-118569400	Weak transcription	Brain Anterior Caudate	brain
24	chr12:118559400-118569400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:118559400-118569800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:118559400-118572600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:118559400-118572800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:118560800-118572800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:118561600-118572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:118561600-118573000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:118562800-118569400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:118563200-118573400	Weak transcription	Lung	lung
33	chr12:118564200-118569400	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:118564200-118572800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:118564400-118569400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:118564400-118569400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:118564400-118573200	Weak transcription	Fetal Stomach	stomach
38	chr12:118565000-118569600	Weak transcription	Ovary	ovary
39	chr12:118565000-118572800	Weak transcription	Gastric	stomach
40	chr12:118565200-118569800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:118565200-118572800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:118565400-118569400	Weak transcription	Liver	Liver
43	chr12:118565400-118569400	Weak transcription	Pancreas	Pancrea
44	chr12:118565600-118569600	Weak transcription	Stomach Mucosa	stomach
45	chr12:118566200-118569600	Weak transcription	Psoas Muscle	Psoas
46	chr12:118566800-118573200	Weak transcription	Right Atrium	heart
47	chr12:118567400-118573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:118568800-118570000	Enhancers	Hela-S3	cervix
49	chr12:118569200-118569600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:118569200-118570200	Enhancers	Brain Substantia Nigra	brain

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