Variant report

Variant	rs11569291
Chromosome Location	chr3:141669685-141669686
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	chr3:141666496-141671385	K562	blood:	n/a	n/a
2	POLR2A	chr3:141669223-141669871	K562	blood:	n/a	n/a
3	POLR2A	chr3:141669581-141669704	H1-hESC	embryonic stem cell:	n/a	n/a
4	EBF1	chr3:141669412-141670034	GM12878	blood:	n/a	chr3:141669606-141669617 chr3:141669607-141669617
5	EBF1	chr3:141669345-141670113	GM12878	blood:	n/a	chr3:141669606-141669617 chr3:141669607-141669617
6	EBF1	chr3:141669396-141669730	GM12878	blood:	n/a	chr3:141669606-141669617 chr3:141669607-141669617
7	POLR2A	chr3:141669535-141669748	K562	blood:	n/a	n/a
8	POLR2A	chr3:141668985-141670156	K562	blood:	n/a	n/a
9	POLR2A	chr3:141669564-141669705	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141457092..141459508-chr3:141668965..141671561,2	K562	blood:
2	chr3:141664146..141666902-chr3:141667918..141670040,2	K562	blood:
3	chr3:141662334..141665277-chr3:141666881..141671768,4	K562	blood:
4	chr3:141457092..141459436-chr3:141668965..141671199,2	K562	blood:

Variant related genes	Relation type
ENSG00000269905	TF binding region
ENSG00000269905	Chromatin interaction
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10935446	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10935447	0.94[EUR][1000 genomes]
rs11569186	1.00[CEU][hapmap]
rs11569190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11569193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11569201	1.00[CEU][hapmap]
rs11569202	1.00[CEU][hapmap]
rs11569205	1.00[CEU][hapmap]
rs11569206	1.00[CEU][hapmap]
rs11569208	1.00[CEU][hapmap]
rs11569209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11569218	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11569220	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11569222	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11569223	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11569259	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11569262	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11569278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11569281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706402	1.00[CEU][hapmap]
rs11706728	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11707100	0.93[EUR][1000 genomes]
rs11708301	1.00[CEU][hapmap]
rs11711748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11712803	1.00[CEU][hapmap]
rs11713023	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11716148	1.00[CEU][hapmap]
rs11717517	1.00[CEU][hapmap]
rs11718167	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11719793	1.00[CEU][hapmap]
rs11844	0.85[EUR][1000 genomes]
rs12487977	0.85[EUR][1000 genomes]
rs12487983	0.85[EUR][1000 genomes]
rs12490893	0.81[EUR][1000 genomes]
rs12493472	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12493495	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12493643	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12494971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12497112	0.94[EUR][1000 genomes]
rs12497443	0.85[EUR][1000 genomes]
rs2288634	0.85[EUR][1000 genomes]
rs2288635	0.85[EUR][1000 genomes]
rs2288636	0.85[EUR][1000 genomes]
rs3762726	0.94[EUR][1000 genomes]
rs3804772	0.85[EUR][1000 genomes]
rs3828398	0.83[EUR][1000 genomes]
rs4683412	0.91[EUR][1000 genomes]
rs4683413	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683414	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683418	1.00[CEU][hapmap]
rs4683649	0.85[EUR][1000 genomes]
rs4683652	0.85[EUR][1000 genomes]
rs4683659	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4683669	1.00[GIH][hapmap]
rs745966	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11569291	ATP1B3	cis	multi-tissue	Pritchard
rs11569291	RBP2	cis	parietal	SCAN
rs11569291	ZBTB38	cis	parietal	SCAN
rs11569291	TFDP2	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
2	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
4	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
6	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:141643000-141675800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:141643400-141671200	Weak transcription	Right Ventricle	heart
9	chr3:141644800-141678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:141647400-141670400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:141647600-141670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:141647800-141670200	Weak transcription	Adipose Nuclei	Adipose
13	chr3:141648000-141670000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:141648000-141670800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:141659200-141696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:141659400-141673800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:141659400-141678400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:141659600-141670400	Weak transcription	NH-A	brain
19	chr3:141659600-141670800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:141659600-141671200	Weak transcription	Pancreas	Pancrea
21	chr3:141659600-141671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:141659600-141674000	Weak transcription	NHLF	lung
23	chr3:141659600-141676000	Weak transcription	Fetal Heart	heart
24	chr3:141659600-141676400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:141659600-141678200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:141659600-141678200	Weak transcription	NHDF-Ad	bronchial
27	chr3:141659600-141678400	Weak transcription	A549	lung
28	chr3:141660000-141670400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:141660000-141670800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:141660000-141673800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:141660000-141674200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:141660200-141670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:141660200-141670800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:141660400-141671200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:141660600-141670200	Weak transcription	Fetal Brain Male	brain
36	chr3:141660600-141698200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:141660800-141670200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:141660800-141670400	Weak transcription	Fetal Brain Female	brain
39	chr3:141660800-141670800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:141661200-141670800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:141661200-141670800	Weak transcription	Gastric	stomach
42	chr3:141661200-141670800	Weak transcription	Lung	lung
43	chr3:141661200-141670800	Weak transcription	Spleen	Spleen
44	chr3:141661400-141670800	Weak transcription	K562	blood
45	chr3:141662400-141670400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:141663400-141672200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:141663400-141674000	Weak transcription	Ovary	ovary
48	chr3:141664200-141672400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:141664200-141672600	Strong transcription	Thymus	Thymus
50	chr3:141664600-141674200	Weak transcription	Esophagus	oesophagus

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