Variant report

Variant	rs557679354
Chromosome Location	chr12:118540922-118540923
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	MAX	chr12:118540886-118541477	ECC-1	luminal epithelium:	n/a	chr12:118541100-118541110 chr12:118541178-118541188
2	MAX	chr12:118540911-118541526	H1-hESC	embryonic stem cell:	n/a	chr12:118541100-118541110 chr12:118541178-118541188
3	MAX	chr12:118540858-118542520	A549	lung:	n/a	chr12:118541100-118541110 chr12:118541778-118541788 chr12:118541178-118541188
4	SIN3A	chr12:118540493-118542395	H1-hESC	embryonic stem cell:	n/a	chr12:118541994-118542007
5	USF2	chr12:118540919-118541092	Hela-S3	cervix:	n/a	n/a
6	MAX	chr12:118540907-118542215	HepG2	liver:	n/a	chr12:118541100-118541110 chr12:118541778-118541788 chr12:118541178-118541188
7	MAX	chr12:118540898-118542371	NB4	blood:	n/a	chr12:118541100-118541110 chr12:118541778-118541788 chr12:118541178-118541188
8	SIN3AK20	chr12:118540801-118541347	A549	lung:	n/a	n/a
9	MAX	chr12:118540867-118542427	MCF-7	breast:	n/a	chr12:118541100-118541110 chr12:118541778-118541788 chr12:118541178-118541188
10	ZKSCAN1	chr12:118539978-118541182	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr12:118540627-118542571	SK-N-SH	brain:	n/a	n/a
12	MAZ	chr12:118540824-118542513	IMR90	lung:	n/a	chr12:118541778-118541788 chr12:118541178-118541188
13	CHD1	chr12:118540672-118541676	H1-hESC	embryonic stem cell:	n/a	n/a
14	CEBPB	chr12:118540763-118542351	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr12:118540834-118542408	MCF-7	breast:	n/a	n/a
16	ZBTB7A	chr12:118540912-118542199	ECC-1	luminal epithelium:	n/a	n/a
17	MAX	chr12:118540849-118541431	SK-N-SH	brain:	n/a	chr12:118541100-118541110 chr12:118541178-118541188
18	MYC	chr12:118540912-118541056	MCF10A-Er-Src	breast:	n/a	n/a
19	TAF1	chr12:118540869-118542112	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:118540838-118542595	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr12:118540828-118542395	Hela-S3	cervix:	n/a	chr12:118541100-118541110 chr12:118541778-118541788 chr12:118541178-118541188
22	MAX	chr12:118540890-118541309	SK-N-SH	brain:	n/a	chr12:118541100-118541110 chr12:118541178-118541188
23	E2F6	chr12:118540871-118542340	A549	lung:	n/a	chr12:118541719-118541728 chr12:118541777-118541789
24	MAX	chr12:118540887-118541447	ECC-1	luminal epithelium:	n/a	chr12:118541100-118541110 chr12:118541178-118541188
25	SMARCC1	chr12:118540881-118542330	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:118540862-118542545	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:118540905-118542496	Hela-S3	cervix:	n/a	n/a
28	TCF7L2	chr12:118540568-118542187	Hela-S3	cervix:	n/a	n/a
29	E2F6	chr12:118540873-118541723	H1-hESC	embryonic stem cell:	n/a	n/a
30	HCFC1	chr12:118540902-118542562	Hela-S3	cervix:	n/a	n/a
31	MXI1	chr12:118540473-118542450	IMR90	lung:	n/a	n/a
32	MAX	chr12:118540891-118542241	A549	lung:	n/a	chr12:118541100-118541110 chr12:118541778-118541788 chr12:118541178-118541188
33	CHD2	chr12:118540915-118542346	Hela-S3	cervix:	n/a	chr12:118541717-118541727
34	MAZ	chr12:118540897-118542147	Hela-S3	cervix:	n/a	chr12:118541778-118541788 chr12:118541178-118541188
35	HA-E2F1	chr12:118540912-118542421	MCF-7	breast:	n/a	chr12:118541719-118541728 chr12:118541793-118541804 chr12:118541777-118541789 chr12:118541777-118541788
36	SMARCB1	chr12:118540866-118542344	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:118540025..118541851-chr12:118573172..118576109,2	MCF-7	breast:
2	chr12:117627165..117629540-chr12:118540302..118543294,2	MCF-7	breast:
3	chr12:118539824..118542719-chr12:118557194..118560231,3	MCF-7	breast:
4	chr12:118490377..118492216-chr12:118538475..118541095,2	MCF-7	breast:
5	chr12:118497389..118502867-chr12:118535601..118543920,23	MCF-7	breast:
6	chr12:118540506..118543698-chr12:118572832..118575450,7	MCF-7	breast:
7	chr12:118498416..118504096-chr12:118537510..118543393,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAOK3-1	chr12:118539412-118540975	NONHSAT031022

Variant related genes	Relation type
VSIG10	TF binding region
ENSG00000176834	Chromatin interaction
ENSG00000135108	Chromatin interaction
ENSG00000089220	Chromatin interaction
ENSG00000176871	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	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
2	nsv560389	chr12:118502467-118564087	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv899546	chr12:118515230-118563982	Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
4	esv3357072	chr12:118540094-118543142	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118501200-118541000	Weak transcription	Aorta	Aorta
2	chr12:118537000-118541000	Weak transcription	Gastric	stomach
3	chr12:118537000-118541000	Weak transcription	Small Intestine	intestine
4	chr12:118539600-118541000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr12:118539800-118542200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:118540000-118541000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:118540000-118541000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr12:118540000-118541000	Flanking Active TSS	Hela-S3	cervix
9	chr12:118540000-118541400	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr12:118540200-118541000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr12:118540200-118542400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr12:118540200-118542600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr12:118540400-118541000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:118540400-118541000	Flanking Active TSS	HMEC	breast
15	chr12:118540400-118541000	Flanking Active TSS	NHEK	skin
16	chr12:118540400-118541200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:118540400-118541200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:118540400-118541200	Flanking Active TSS	Dnd41	blood
19	chr12:118540400-118541600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr12:118540400-118542200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:118540400-118542200	Active TSS	Pancreas	Pancrea
22	chr12:118540400-118542200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr12:118540400-118542400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:118540400-118542400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr12:118540400-118542400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:118540400-118542400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr12:118540400-118542400	Bivalent/Poised TSS	Fetal Brain Female	brain
28	chr12:118540400-118542600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr12:118540400-118542600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr12:118540400-118542600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:118540400-118542600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr12:118540400-118542600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:118540400-118542600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr12:118540600-118541000	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr12:118540600-118541000	Flanking Active TSS	Fetal Lung	lung
36	chr12:118540600-118541000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr12:118540600-118541000	Enhancers	Spleen	Spleen
38	chr12:118540600-118541000	Flanking Active TSS	HUVEC	blood vessel
39	chr12:118540600-118541200	Active TSS	Colonic Mucosa	Colon
40	chr12:118540600-118541400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:118540600-118541800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:118540600-118542000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:118540600-118542000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:118540600-118542200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:118540600-118542200	Active TSS	A549	lung
46	chr12:118540600-118542400	Active TSS	Esophagus	oesophagus
47	chr12:118540600-118542400	Active TSS	Fetal Kidney	kidney
48	chr12:118540600-118542400	Active TSS	HepG2	liver
49	chr12:118540600-118542600	Active TSS	H1 Cell Line	embryonic stem cell
50	chr12:118540600-118542600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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