Variant report

Variant	rs12805109
Chromosome Location	chr11:9023259-9023260
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	POLR2A	chr11:9023184-9023807	HUVEC	blood vessel:	n/a	n/a
2	CUX1	chr11:9023043-9023931	K562	blood:	n/a	n/a
3	CBX3	chr11:9023224-9023690	K562	blood:	n/a	n/a
4	E2F6	chr11:9023232-9023548	K562	blood:	n/a	n/a
5	MXI1	chr11:9022752-9023898	IMR90	lung:	n/a	n/a
6	JUN	chr11:9023027-9024210	K562	blood:	n/a	chr11:9023566-9023574
7	FOS	chr11:9023259-9023755	MCF10A-Er-Src	breast:	n/a	chr11:9023566-9023574 chr11:9023564-9023575
8	E2F6	chr11:9023220-9023601	K562	blood:	n/a	n/a
9	MAX	chr11:9023259-9023577	K562	blood:	n/a	n/a
10	FOSL1	chr11:9023212-9023709	K562	blood:	n/a	chr11:9023566-9023574
11	MAX	chr11:9023257-9023689	HCT-116	colon:	n/a	n/a
12	MAX	chr11:9023249-9023715	NB4	blood:	n/a	n/a
13	TEAD4	chr11:9023237-9024023	K562	blood:	n/a	n/a
14	MAX	chr11:9023257-9023730	SK-N-SH	brain:	n/a	n/a
15	MAX	chr11:9023197-9023685	K562	blood:	n/a	n/a
16	FOS	chr11:9023205-9023790	HUVEC	blood vessel:	n/a	chr11:9023566-9023574 chr11:9023564-9023575

No.	Distal block	Cell Line	Cell type
1	chr11:9022966..9025427-chr11:9154942..9157918,2	K562	blood:
2	chr11:9020957..9023609-chr11:9034116..9037224,3	K562	blood:
3	chr11:9023067..9025427-chr11:9156418..9158861,2	K562	blood:
4	chr11:8996724..8999605-chr11:9022687..9025353,2	K562	blood:

Variant related genes	Relation type
ENSG00000253973	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10219366	0.81[EUR][1000 genomes]
rs10769976	0.83[EUR][1000 genomes]
rs10840156	0.83[EUR][1000 genomes]
rs12785559	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786377	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790020	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794962	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12798311	0.80[EUR][1000 genomes]
rs1347016	0.87[ASN][1000 genomes]
rs1985026	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016844	0.81[EUR][1000 genomes]
rs2056903	0.81[EUR][1000 genomes]
rs2116510	0.87[ASN][1000 genomes]
rs2116511	0.87[ASN][1000 genomes]
rs2246878	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247038	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2252102	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316541	0.85[ASN][1000 genomes]
rs2568047	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568069	0.87[ASN][1000 genomes]
rs2568074	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568075	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568077	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568079	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568081	0.85[ASN][1000 genomes]
rs2568086	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568087	0.87[ASN][1000 genomes]
rs2568088	0.81[ASN][1000 genomes]
rs2653590	0.87[ASN][1000 genomes]
rs2653601	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2653604	0.87[ASN][1000 genomes]
rs2653611	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742473	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742486	0.87[ASN][1000 genomes]
rs2742487	0.87[ASN][1000 genomes]
rs2742488	0.87[ASN][1000 genomes]
rs2742489	0.81[ASN][1000 genomes]
rs2742491	0.87[ASN][1000 genomes]
rs2742493	0.87[ASN][1000 genomes]
rs2742495	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742496	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2742497	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742504	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742505	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742512	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742513	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742514	0.81[ASN][1000 genomes]
rs3751063	0.83[EUR][1000 genomes]
rs4264185	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4370967	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4909951	0.83[EUR][1000 genomes]
rs4910313	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486061	0.83[AMR][1000 genomes]
rs66630602	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7124403	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852790	0.85[ASN][1000 genomes]
rs72853712	0.85[ASN][1000 genomes]
rs7940895	0.87[ASN][1000 genomes]
rs909464	0.81[EUR][1000 genomes]
rs9300096	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	esv3477864	chr11:9023195-9023500	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12805109	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs12805109	C11orf17	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9020200-9023400	Weak transcription	Gastric	stomach
2	chr11:9022600-9024600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:9022800-9023400	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr11:9022800-9023600	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr11:9022800-9024400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:9022800-9024600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr11:9023000-9023400	Bivalent Enhancer	Primary B cells from cord blood	blood
8	chr11:9023000-9023400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:9023000-9023600	Flanking Active TSS	K562	blood
10	chr11:9023000-9023600	Enhancers	NHLF	lung
11	chr11:9023000-9023800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:9023000-9024200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:9023000-9024400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:9023000-9024400	Enhancers	Osteobl	bone
15	chr11:9023000-9024600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:9023000-9024600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:9023200-9023400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
18	chr11:9023200-9023400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:9023200-9023400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:9023200-9023400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:9023200-9023600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:9023200-9023600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:9023200-9023600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr11:9023200-9023600	ZNF genes & repeats	Pancreas	Pancrea
25	chr11:9023200-9023600	Enhancers	Hela-S3	cervix
26	chr11:9023200-9023600	Enhancers	NH-A	brain
27	chr11:9023200-9023600	Flanking Active TSS	NHDF-Ad	bronchial
28	chr11:9023200-9023800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:9023200-9024000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr11:9023200-9024200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:9023200-9024200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:9023200-9024400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:9023200-9024400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr11:9023200-9024400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:9023200-9024600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:9023200-9024600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
37	chr11:9023200-9024600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr11:9023200-9024600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:9023200-9024600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:9023200-9024600	Enhancers	HMEC	breast
41	chr11:9023200-9024600	Enhancers	HSMM	muscle
42	chr11:9023200-9024600	Enhancers	HUVEC	blood vessel
43	chr11:9023200-9024600	Enhancers	NHEK	skin
44	chr11:9023200-9025000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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