Variant report

Variant	rs1790476
Chromosome Location	chr11:120008957-120008958
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr11:120008530-120009147	MCF-7	breast:	n/a	n/a
2	MYC	chr11:120008717-120009156	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr11:120008540-120008960	NHEK	skin:	n/a	n/a
4	ZNF263	chr11:120008622-120009082	HEK293-T-REx	kidney:	n/a	n/a
5	SMC3	chr11:120008388-120009115	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr11:120008686-120009274	ECC-1	luminal epithelium:	n/a	n/a
7	E2F4	chr11:120008778-120009103	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr11:120008613-120008997	Hela-S3	cervix:	n/a	n/a
9	MAX	chr11:120008710-120009080	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr11:120008475-120009011	Hela-S3	cervix:	n/a	n/a
11	MYC	chr11:120008659-120009216	MCF10A-Er-Src	breast:	n/a	n/a
12	CHD2	chr11:120008385-120008992	Hela-S3	cervix:	n/a	n/a
13	GTF2F1	chr11:120008481-120009221	Hela-S3	cervix:	n/a	n/a
14	MYC	chr11:120008724-120009005	MCF-7	breast:	n/a	n/a
15	MAZ	chr11:120008454-120009113	Hela-S3	cervix:	n/a	n/a
16	MAX	chr11:120008580-120009122	MCF-7	breast:	n/a	n/a
17	POLR2A	chr11:120008527-120009020	MCF-7	breast:	n/a	n/a
18	POLR2A	chr11:120008572-120009228	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr11:120008708-120009013	MCF-7	breast:	n/a	n/a
20	MAX	chr11:120007803-120009040	Hela-S3	cervix:	n/a	n/a
21	SMARCB1	chr11:120007876-120009165	Hela-S3	cervix:	n/a	n/a
22	NR2F2	chr11:120008589-120009158	MCF-7	breast:	n/a	n/a
23	RCOR1	chr11:120008558-120009218	Hela-S3	cervix:	n/a	n/a
24	RFX5	chr11:120007105-120009011	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr11:120008466-120009012	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr11:120008559-120008999	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:120008944-120008994	BE2_C	brain:	n/a
2	chr11:120008944-120008994	HCT-116	colon:	n/a
3	chr11:120008944-120008994	AG09319	gingival:	n/a
4	chr11:120008944-120008994	H1-hESC	embryonic stem cell:	embryo
5	chr11:120008944-120008994	NHBE	bronchial:	n/a
6	chr11:120008944-120008994	LNCaP	prostate:	n/a
7	chr11:120008944-120008994	Hela-S3	cervix:	n/a
8	chr11:120008944-120008994	GM12891	blood:	n/a
9	chr11:120008944-120008994	HepG2	liver:	n/a
10	chr11:120008944-120008994	IMR90	lung:	fetal
11	chr11:120008944-120008994	CMK	blood:	n/a
12	chr11:120008944-120008994	HRPEpiC	eye:	n/a
13	chr11:120008944-120008994	HAEpiC	amniotic membrane:	n/a
14	chr11:120008944-120008994	MCF-7	breast:	n/a
15	chr11:120008944-120008994	HEEpiC	esophagus:	n/a
16	chr11:120008944-120008994	HEK293	kidney:	embryo
17	chr11:120008944-120008994	MCF10A-Er-Src	breast:	n/a
18	chr11:120008944-120008994	ovcar-3	ovarian:	n/a
19	chr11:120008944-120008994	HPAEpiC	pulmonary alveolar:	n/a
20	chr11:120008944-120008994	AG09309	skin:	n/a
21	chr11:120008944-120008994	ECC-1	luminal epithelium:	n/a
22	chr11:120008944-120008994	K562	blood:	n/a
23	chr11:120008944-120008994	PANC-1	pancreas:	n/a
24	chr11:120008944-120008994	PrEC	prostate:	n/a
25	chr11:120008944-120008994	SAEC	small airway:	n/a
26	chr11:120008944-120008994	Caco-2	colon:	n/a
27	chr11:120008944-120008994	AoSMC	blood vessel:	n/a
28	chr11:120008944-120008994	SK-N-MC	brain:	n/a
29	chr11:120008944-120008994	HCPEpiC	choroid plexus:	n/a
30	chr11:120008944-120008994	Hepatocyte	liver:	n/a
31	chr11:120008944-120008994	NHDF-neo	bronchial:	n/a
32	chr11:120008944-120008994	GM12892	blood:	n/a
33	chr11:120008944-120008994	HIPEpiC	eye:	n/a
34	chr11:120008944-120008994	A549	lung:	n/a
35	chr11:120008944-120008994	HMEC	breast:	n/a
36	chr11:120008944-120008994	HUVEC	blood vessel:	n/a
37	chr11:120008944-120008994	NH-A	brain:	n/a
38	chr11:120008944-120008994	AG04450	lung:	fetal
39	chr11:120008944-120008994	T-47D	breast:	n/a
40	chr11:120008944-120008994	PFSK-1	brain:	n/a
41	chr11:120008944-120008994	HRCEpiC	kidney:	n/a
42	chr11:120008944-120008994	HCM	heart:	n/a
43	chr11:120008944-120008994	SK-N-SH_RA	brain:	n/a
44	chr11:120008944-120008994	AG04449	skin:	fetal
45	chr11:120008944-120008994	AG10803	skin:	n/a
46	chr11:120008944-120008994	HL-60	blood:	n/a
47	chr11:120008944-120008994	BJ	skin:	n/a
48	chr11:120008944-120008994	HCF	heart:	n/a
49	chr11:120008944-120008994	SK-N-SH	brain:	n/a
50	chr11:120008944-120008994	ProgFib	skin:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:119990134..119993227-chr11:120007102..120010731,5	MCF-7	breast:
2	chr11:120008416..120009260-chr17:42143798..42144484,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
TRIM29	TF binding region
TRIM29	CpG island
ENSG00000137699	Chromatin interaction
ENSG00000161654	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs470411	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs470725	0.85[EUR][1000 genomes]
rs470941	0.85[EUR][1000 genomes]
rs488672	0.90[EUR][1000 genomes]
rs531260	0.90[EUR][1000 genomes]
rs550164	0.89[EUR][1000 genomes]
rs561498	0.89[EUR][1000 genomes]
rs605374	0.97[EUR][1000 genomes]
rs896691	0.80[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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1790476	TRIM29	cis	Artery Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120006600-120009000	Active TSS	HMEC	breast
2	chr11:120006600-120009200	Active TSS	NHEK	skin
3	chr11:120006800-120009000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr11:120007000-120009000	Active TSS	Hela-S3	cervix
5	chr11:120007200-120021400	Weak transcription	Right Atrium	heart
6	chr11:120007800-120010200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:120008200-120009200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:120008400-120009000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:120008400-120009200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:120008400-120009200	Enhancers	Stomach Mucosa	stomach
11	chr11:120008400-120009400	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr11:120008400-120009400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr11:120008600-120009200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:120008600-120009400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr11:120008800-120009000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:120008800-120009000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:120008800-120009600	Weak transcription	Esophagus	oesophagus
18	chr11:120008800-120010200	Enhancers	Placenta	Placenta
19	chr11:120008800-120010600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links