Variant report

Variant	rs6490170
Chromosome Location	chr12:118569822-118569823
allele	C/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	RUNX3	chr12:118569748-118570294	GM12878	blood:	n/a	n/a
2	MAX	chr12:118569704-118570252	MCF-7	breast:	n/a	chr12:118570073-118570082
3	RUNX3	chr12:118569775-118570161	GM12878	blood:	n/a	n/a
4	FOXA1	chr12:118569739-118570299	HepG2	liver:	n/a	chr12:118569981-118569993
5	MXI1	chr12:118569293-118570247	HepG2	liver:	n/a	n/a
6	TEAD4	chr12:118569713-118570289	HepG2	liver:	n/a	n/a
7	SP1	chr12:118569686-118570267	HepG2	liver:	n/a	n/a
8	NFIC	chr12:118569165-118570311	HepG2	liver:	n/a	chr12:118569438-118569455 chr12:118569924-118569940 chr12:118569924-118569941 chr12:118569438-118569454
9	TEAD4	chr12:118569650-118570109	ECC-1	luminal epithelium:	n/a	n/a
10	MYBL2	chr12:118569142-118570329	HepG2	liver:	n/a	n/a
11	RXRA	chr12:118569669-118570356	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:118569788-118569889	GM12878	blood:	n/a	n/a
13	NFIC	chr12:118569180-118570265	ECC-1	luminal epithelium:	n/a	chr12:118569438-118569455 chr12:118569924-118569940 chr12:118569924-118569941 chr12:118569438-118569454
14	TCF12	chr12:118569349-118570194	ECC-1	luminal epithelium:	n/a	n/a
15	TEAD4	chr12:118569260-118570184	ECC-1	luminal epithelium:	n/a	n/a
16	FOXA2	chr12:118569811-118570242	HepG2	liver:	n/a	chr12:118569981-118569993
17	KAP1	chr12:118569407-118570198	HEK293	kidney:	n/a	n/a
18	MAX	chr12:118569804-118570241	ECC-1	luminal epithelium:	n/a	chr12:118570073-118570082
19	MAX	chr12:118569788-118570231	HepG2	liver:	n/a	chr12:118570073-118570082
20	HEY1	chr12:118569783-118570277	HepG2	liver:	n/a	n/a
21	EP300	chr12:118569620-118570295	HepG2	liver:	n/a	n/a
22	CEBPB	chr12:118569760-118570055	HepG2	liver:	n/a	n/a
23	MYBL2	chr12:118569751-118570295	HepG2	liver:	n/a	n/a
24	KAP1	chr12:118569378-118570321	U2OS	brain:	n/a	n/a
25	FOXA1	chr12:118569769-118570289	HepG2	liver:	n/a	chr12:118569981-118569993
26	TCF12	chr12:118569611-118570151	ECC-1	luminal epithelium:	n/a	n/a
27	ARID3A	chr12:118569744-118570346	HepG2	liver:	n/a	n/a
28	EP300	chr12:118569634-118570369	HepG2	liver:	n/a	n/a
29	EP300	chr12:118569256-118570179	ECC-1	luminal epithelium:	n/a	chr12:118569341-118569355 chr12:118569342-118569356
30	NR2F2	chr12:118569549-118570123	MCF-7	breast:	n/a	n/a
31	MAX	chr12:118569664-118570331	HepG2	liver:	n/a	chr12:118570073-118570082
32	NFIC	chr12:118569195-118570185	ECC-1	luminal epithelium:	n/a	chr12:118569438-118569455 chr12:118569924-118569940 chr12:118569924-118569941 chr12:118569438-118569454
33	TCF12	chr12:118569729-118570354	A549	lung:	n/a	n/a
34	NFIC	chr12:118569773-118570120	HepG2	liver:	n/a	chr12:118569924-118569940 chr12:118569924-118569941
35	HDAC2	chr12:118569815-118570123	MCF-7	breast:	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
ENSG00000176834	Chromatin interaction
ENSG00000089220	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3847651	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973195	0.86[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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118542600-118572800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr12:118542600-118573400	Weak transcription	Primary T cells from cord blood	blood
3	chr12:118552800-118572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:118552800-118573400	Weak transcription	Aorta	Aorta
5	chr12:118553000-118573000	Weak transcription	Fetal Brain Female	brain
6	chr12:118558800-118572800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:118559200-118570000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:118559200-118572600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:118559200-118572600	Weak transcription	NHEK	skin
10	chr12:118559200-118572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:118559200-118573000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:118559200-118573000	Weak transcription	Fetal Kidney	kidney
13	chr12:118559200-118573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:118559200-118573400	Weak transcription	Fetal Intestine Small	intestine
15	chr12:118559400-118572600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:118559400-118572800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:118560800-118572800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:118561600-118572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:118561600-118573000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:118563200-118573400	Weak transcription	Lung	lung
21	chr12:118564200-118572800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:118564400-118573200	Weak transcription	Fetal Stomach	stomach
23	chr12:118565000-118572800	Weak transcription	Gastric	stomach
24	chr12:118565200-118572800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:118566800-118573200	Weak transcription	Right Atrium	heart
26	chr12:118567400-118573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:118568800-118570000	Enhancers	Hela-S3	cervix
28	chr12:118569200-118570200	Enhancers	Brain Substantia Nigra	brain
29	chr12:118569200-118570200	Flanking Active TSS	A549	lung
30	chr12:118569200-118570400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:118569200-118570400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:118569200-118570600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr12:118569200-118570600	Flanking Active TSS	HepG2	liver
34	chr12:118569400-118570000	Enhancers	Fetal Muscle Trunk	muscle
35	chr12:118569400-118570200	Enhancers	Fetal Muscle Leg	muscle
36	chr12:118569400-118570200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr12:118569400-118570400	Enhancers	Adipose Nuclei	Adipose
38	chr12:118569400-118570400	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr12:118569400-118570600	Enhancers	Pancreas	Pancrea
40	chr12:118569400-118570800	Enhancers	Dnd41	blood
41	chr12:118569400-118572600	Enhancers	Liver	Liver
42	chr12:118569600-118570000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:118569600-118570000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:118569600-118570200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:118569600-118570200	Enhancers	Brain Germinal Matrix	brain
46	chr12:118569600-118570200	Enhancers	Brain Hippocampus Middle	brain
47	chr12:118569600-118570200	Enhancers	Colonic Mucosa	Colon
48	chr12:118569600-118570200	Enhancers	Ovary	ovary
49	chr12:118569600-118570200	Enhancers	Psoas Muscle	Psoas
50	chr12:118569600-118570200	Enhancers	Stomach Mucosa	stomach

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