Variant report

Variant	rs10965049
Chromosome Location	chr9:21526526-21526527
allele	C/G
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	FOSL1	chr9:21524822-21527232	HCT-116	colon:	n/a	n/a
2	CBX3	chr9:21526174-21527163	HCT-116	colon:	n/a	n/a
3	JUND	chr9:21519231-21528507	HCT-116	colon:	n/a	n/a
4	POLR2A	chr9:21519358-21529034	PANC-1	pancreas:	n/a	n/a
5	JUND	chr9:21517910-21528426	HCT-116	colon:	n/a	n/a
6	POLR2A	chr9:21526326-21526594	Hela-S3	cervix:	n/a	n/a
7	ELF1	chr9:21519892-21526918	HCT-116	colon:	n/a	n/a
8	SRF	chr9:21519933-21527253	HCT-116	colon:	n/a	n/a
9	POLR2A	chr9:21515900-21530251	A549	lung:	n/a	n/a
10	POLR2A	chr9:21525952-21526918	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr9:21516566-21534519	HCT-116	colon:	n/a	n/a
12	POLR2A	chr9:21519394-21529027	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
ENSG00000264379	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10811557	0.88[GIH][hapmap]
rs10811562	0.97[ASN][1000 genomes]
rs10811563	0.98[ASN][1000 genomes]
rs10811564	0.97[ASN][1000 genomes]
rs10811565	0.86[ASN][1000 genomes]
rs10811566	0.87[ASN][1000 genomes]
rs10811568	0.92[ASN][1000 genomes]
rs10965041	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10965050	0.99[ASN][1000 genomes]
rs10965053	0.98[ASN][1000 genomes]
rs10965054	0.95[ASN][1000 genomes]
rs10965060	0.83[ASN][1000 genomes]
rs12378286	0.95[ASN][1000 genomes]
rs12378990	0.95[ASN][1000 genomes]
rs12379382	0.95[ASN][1000 genomes]
rs12379709	0.95[ASN][1000 genomes]
rs12379721	0.95[ASN][1000 genomes]
rs16938448	0.95[ASN][1000 genomes]
rs55683539	0.95[ASN][1000 genomes]
rs72703447	0.99[ASN][1000 genomes]
rs72703448	0.97[ASN][1000 genomes]
rs72703449	0.96[ASN][1000 genomes]
rs72703450	0.97[ASN][1000 genomes]
rs9644855	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
2	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
4	esv2757326	chr9:21499624-21526526	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA	105 gene(s)	inside rSNPs	diseases
5	esv2759680	chr9:21499624-21526526	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA	105 gene(s)	inside rSNPs	diseases
6	nsv892741	chr9:21517302-21551513	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10965049	KIAA0355	trans	brain	seeQTL
rs10965049	TBP	trans	cerebellum	SCAN
rs10965049	UTS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21466000-21527600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:21494800-21527600	Weak transcription	Gastric	stomach
3	chr9:21507200-21551400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:21507400-21527200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:21508000-21542000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:21508200-21527600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:21508200-21527600	Weak transcription	Fetal Intestine Small	intestine
8	chr9:21510400-21527600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:21512200-21526600	Weak transcription	HSMM	muscle
10	chr9:21512800-21527000	Weak transcription	NHLF	lung
11	chr9:21513000-21526600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:21514400-21527000	Weak transcription	Hela-S3	cervix
13	chr9:21516800-21542600	Weak transcription	Stomach Mucosa	stomach
14	chr9:21520400-21526600	Weak transcription	HUVEC	blood vessel
15	chr9:21520400-21526800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:21520400-21527000	Weak transcription	NHDF-Ad	bronchial
17	chr9:21522600-21532600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:21522600-21533200	Strong transcription	NH-A	brain
19	chr9:21522800-21530000	ZNF genes & repeats	A549	lung
20	chr9:21523400-21527400	Weak transcription	Fetal Intestine Large	intestine
21	chr9:21523600-21527600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:21524000-21527800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:21524400-21527600	Strong transcription	HMEC	breast
24	chr9:21524400-21532200	Strong transcription	Osteobl	bone
25	chr9:21525400-21527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:21525600-21534000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:21525800-21530800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr9:21526000-21527800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:21526200-21527400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:21526200-21527600	Weak transcription	Fetal Stomach	stomach
31	chr9:21526200-21532400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:21526400-21527600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:21526400-21527600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr9:21526400-21528000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:21526400-21529600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:21526400-21530000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:21526400-21534800	Strong transcription	NHEK	skin

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