Variant report

Variant	rs11242769
Chromosome Location	chr6:2433054-2433055
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	RAD21	chr6:2432552-2433116	IMR90	lung:	n/a	n/a
2	RCOR1	chr6:2431979-2433326	IMR90	lung:	n/a	n/a
3	MAZ	chr6:2432094-2433268	IMR90	lung:	n/a	n/a
4	EP300	chr6:2432216-2433430	ECC-1	luminal epithelium:	n/a	n/a
5	JUND	chr6:2432082-2433191	SK-N-SH	brain:	n/a	chr6:2432643-2432654 chr6:2433036-2433045
6	TCF12	chr6:2432386-2433054	SK-N-SH	brain:	n/a	chr6:2432717-2432725
7	MXI1	chr6:2432204-2433712	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000272465	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10458063	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10458138	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10458139	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10458140	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458141	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10458142	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11242766	0.80[AMR][1000 genomes]
rs11242770	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242772	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs11242773	0.86[EUR][1000 genomes]
rs11242775	0.83[EUR][1000 genomes]
rs11753825	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11758482	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12189681	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12189724	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs12195877	0.83[EUR][1000 genomes]
rs12196223	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12199363	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12199637	0.82[EUR][1000 genomes]
rs12205452	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206851	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12209220	0.83[EUR][1000 genomes]
rs12209322	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209326	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12210286	0.83[EUR][1000 genomes]
rs12210452	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12213643	0.83[EUR][1000 genomes]
rs12528202	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662045	0.85[EUR][1000 genomes]
rs13214565	0.85[EUR][1000 genomes]
rs13220392	0.85[EUR][1000 genomes]
rs2073003	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076470	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294659	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34885387	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35144026	0.83[EUR][1000 genomes]
rs3734506	0.85[EUR][1000 genomes]
rs3817904	0.80[CHB][hapmap];0.85[EUR][1000 genomes]
rs9328099	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs982096	0.90[EUR][1000 genomes]
rs983027	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs983028	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2399800-2449200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:2402200-2449200	Weak transcription	Left Ventricle	heart
3	chr6:2414600-2434600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:2414600-2452000	Weak transcription	Ovary	ovary
5	chr6:2414800-2448800	Weak transcription	Liver	Liver
6	chr6:2414800-2449200	Weak transcription	Fetal Stomach	stomach
7	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
8	chr6:2426400-2439800	Weak transcription	Aorta	Aorta
9	chr6:2428800-2446200	Weak transcription	Right Ventricle	heart
10	chr6:2430600-2434000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:2431000-2434800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:2431200-2434800	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:2431400-2435400	Enhancers	HMEC	breast
14	chr6:2431600-2434000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:2431600-2439800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:2431800-2435800	Enhancers	Esophagus	oesophagus
17	chr6:2432000-2433400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:2432000-2433400	Enhancers	HSMM	muscle
19	chr6:2432000-2433400	Enhancers	NHDF-Ad	bronchial
20	chr6:2432000-2433400	Enhancers	Osteobl	bone
21	chr6:2432000-2433600	Enhancers	HSMMtube	muscle
22	chr6:2432000-2433800	Enhancers	NH-A	brain
23	chr6:2432000-2434400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:2432000-2435000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:2432000-2435200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:2432200-2433600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:2432200-2435000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:2432200-2435000	Enhancers	NHEK	skin
29	chr6:2432200-2435400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:2432200-2449200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:2432400-2433200	Enhancers	NHLF	lung
32	chr6:2432400-2435000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:2432600-2433800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:2432600-2434200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:2432800-2433200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:2432800-2433200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:2432800-2434800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:2433000-2433800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:2433000-2434000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:2433000-2434000	Weak transcription	Placenta	Placenta
41	chr6:2433000-2434800	Enhancers	Fetal Thymus	thymus

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