Variant report

Variant	rs11141404
Chromosome Location	chr9:72658280-72658281
allele	A/C
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	TEAD4	chr9:72658147-72658655	H1-hESC	embryonic stem cell:	n/a	chr9:72658388-72658397
2	YY1	chr9:72658238-72658679	H1-hESC	embryonic stem cell:	n/a	chr9:72658635-72658646
3	NANOG	chr9:72658179-72658486	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr9:72658107-72658504	ECC-1	luminal epithelium:	n/a	chr9:72658388-72658397
5	CHD2	chr9:72658232-72658982	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:72658257-72659250	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr9:72658217-72658411	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr9:72658077-72658605	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr9:72657997-72660251	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr9:72658173-72658549	H1-hESC	embryonic stem cell:	n/a	chr9:72658421-72658429
11	TEAD4	chr9:72658236-72658657	ECC-1	luminal epithelium:	n/a	chr9:72658388-72658397
12	ATF2	chr9:72658141-72658540	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTBP2	chr9:72658276-72660027	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr9:72658084-72658659	H1-hESC	embryonic stem cell:	n/a	chr9:72658388-72658397

Variant related genes	Relation type
MAMDC2	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10780773	0.86[ASN][1000 genomes]
rs10868453	0.86[ASN][1000 genomes]
rs10868475	0.82[ASN][1000 genomes]
rs10868485	0.83[ASN][1000 genomes]
rs11141507	0.82[ASN][1000 genomes]
rs2975923	0.82[EUR][1000 genomes]
rs2997658	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4543602	0.86[ASN][1000 genomes]
rs6559939	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72653400-72658400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:72653600-72658400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:72653600-72658400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:72653600-72658400	Weak transcription	Colonic Mucosa	Colon
5	chr9:72656600-72658400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:72656600-72658600	Enhancers	Esophagus	oesophagus
7	chr9:72657000-72658400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:72657200-72658400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:72657200-72658400	Flanking Active TSS	Colon Smooth Muscle	Colon
10	chr9:72657200-72658600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:72657200-72658600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:72657400-72658400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr9:72657400-72658400	Enhancers	Brain Hippocampus Middle	brain
14	chr9:72657600-72658400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:72657600-72658400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:72657800-72658400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:72657800-72658400	Enhancers	Fetal Heart	heart
18	chr9:72657800-72658400	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr9:72657800-72658400	Flanking Active TSS	HSMMtube	muscle
20	chr9:72657800-72658600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:72657800-72658600	Bivalent Enhancer	Placenta	Placenta
22	chr9:72657800-72659000	Flanking Active TSS	HSMM	muscle
23	chr9:72657800-72660400	Flanking Active TSS	HMEC	breast
24	chr9:72658000-72658400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:72658000-72658400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr9:72658000-72658400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr9:72658000-72658400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:72658000-72658400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr9:72658000-72658400	Weak transcription	Spleen	Spleen
30	chr9:72658000-72658600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:72658000-72658600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:72658000-72658600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
33	chr9:72658000-72658800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr9:72658000-72659200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:72658000-72659200	Flanking Active TSS	NHEK	skin
36	chr9:72658000-72660000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr9:72658000-72660200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:72658000-72661000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
39	chr9:72658200-72658400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:72658200-72658400	Bivalent Enhancer	Brain Anterior Caudate	brain
41	chr9:72658200-72658400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
42	chr9:72658200-72658400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr9:72658200-72658400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:72658200-72658400	Bivalent Enhancer	Fetal Brain Female	brain
45	chr9:72658200-72658400	Enhancers	Psoas Muscle	Psoas
46	chr9:72658200-72658400	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr9:72658200-72658400	Flanking Active TSS	Right Ventricle	heart
48	chr9:72658200-72658400	Enhancers	Osteobl	bone
49	chr9:72658200-72658600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr9:72658200-72658600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links