Variant report

Variant	rs12278345
Chromosome Location	chr11:120058685-120058686
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	GATA3	chr11:120058538-120058738	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
TRIM29	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10892546	0.95[ASN][1000 genomes]
rs10892547	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12273399	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790943	0.96[EUR][1000 genomes]
rs12791292	0.96[EUR][1000 genomes]
rs2444239	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs481599	0.95[ASN][1000 genomes]
rs507419	0.95[ASN][1000 genomes]
rs508205	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs508266	0.95[ASN][1000 genomes]
rs513638	0.95[ASN][1000 genomes]
rs7116997	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896693	0.91[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	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
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120049400-120059800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr11:120055400-120058800	Enhancers	NHLF	lung
3	chr11:120055400-120059400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:120055600-120059000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:120055800-120059000	Enhancers	Small Intestine	intestine
6	chr11:120055800-120059400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:120056000-120060200	Enhancers	Ovary	ovary
8	chr11:120056000-120064600	Enhancers	Fetal Stomach	stomach
9	chr11:120056200-120058800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:120056200-120059200	Enhancers	Fetal Intestine Large	intestine
11	chr11:120056200-120060800	Enhancers	Pancreas	Pancrea
12	chr11:120056400-120059000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr11:120056400-120060200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr11:120056800-120059600	Enhancers	Duodenum Mucosa	Duodenum
15	chr11:120057000-120059400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr11:120057400-120058800	Enhancers	Brain Angular Gyrus	brain
17	chr11:120057600-120058800	Enhancers	Fetal Heart	heart
18	chr11:120057600-120059200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:120057600-120059200	Active TSS	Rectal Smooth Muscle	rectum
20	chr11:120057800-120058800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr11:120057800-120063600	Enhancers	HepG2	liver
22	chr11:120058000-120058800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:120058000-120068800	Weak transcription	Right Atrium	heart
24	chr11:120058200-120058800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr11:120058200-120058800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:120058200-120058800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr11:120058200-120058800	Flanking Active TSS	Fetal Lung	lung
28	chr11:120058200-120058800	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr11:120058200-120059000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr11:120058200-120059000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:120058200-120059000	Enhancers	Fetal Brain Female	brain
32	chr11:120058200-120059200	Weak transcription	Right Ventricle	heart
33	chr11:120058200-120061600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:120058200-120063800	Weak transcription	Gastric	stomach
35	chr11:120058200-120068200	Weak transcription	Spleen	Spleen
36	chr11:120058400-120058800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
37	chr11:120058400-120058800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
38	chr11:120058400-120058800	Enhancers	Adipose Nuclei	Adipose
39	chr11:120058400-120059000	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr11:120058400-120059200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:120058400-120060000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr11:120058400-120061200	Enhancers	Stomach Mucosa	stomach
43	chr11:120058400-120061400	Enhancers	Colonic Mucosa	Colon
44	chr11:120058400-120061800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr11:120058400-120062000	Weak transcription	Fetal Brain Male	brain
46	chr11:120058400-120066400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:120058400-120066600	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:120058400-120066800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr11:120058600-120058800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:120058600-120059000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links