Variant report

Variant	rs6041768
Chromosome Location	chr20:12999157-12999158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1549824	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16993660	1.00[EUR][1000 genomes]
rs171499	0.94[EUR][1000 genomes]
rs17226299	0.89[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17226306	0.89[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17226313	0.89[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17812078	0.89[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17812085	0.89[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17812091	0.89[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17812097	0.89[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3848768	1.00[ASW][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap];0.84[EUR][1000 genomes]
rs4555414	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56022742	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6033565	1.00[AFR][1000 genomes]
rs6033566	1.00[AFR][1000 genomes]
rs6033569	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6033573	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6033575	1.00[EUR][1000 genomes]
rs6033592	0.82[EUR][1000 genomes]
rs6041751	1.00[AFR][1000 genomes]
rs6041757	0.91[AMR][1000 genomes]
rs6041760	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6041766	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6041776	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6041777	0.89[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs6109665	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs673694	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833923	chr20:12904689-13064426	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv833924	chr20:12997093-13189239	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12991200-13001400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:12991200-13002800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr20:12991200-13003200	Weak transcription	Ovary	ovary
4	chr20:12991200-13003600	Weak transcription	Pancreas	Pancrea
5	chr20:12991400-13002400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:12991800-13001600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:12992000-13002200	Weak transcription	Aorta	Aorta
8	chr20:12992200-13000400	Weak transcription	Stomach Mucosa	stomach
9	chr20:12992200-13000800	Weak transcription	NHEK	skin
10	chr20:12992400-13001000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:12993400-13001400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr20:12993800-13001400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:12994000-13002200	Weak transcription	Thymus	Thymus
14	chr20:12994600-13001600	Weak transcription	Fetal Kidney	kidney
15	chr20:12994600-13003000	Weak transcription	Left Ventricle	heart
16	chr20:12995800-13001600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr20:12996200-13001600	Weak transcription	Liver	Liver
18	chr20:12997200-12999800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr20:12997600-12999200	Enhancers	Osteobl	bone
20	chr20:12997600-13003800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:12997800-13003000	Weak transcription	Right Atrium	heart
22	chr20:12997800-13008200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr20:12998600-13002200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr20:12998600-13002600	Strong transcription	Placenta	Placenta
25	chr20:12998800-12999400	Weak transcription	Fetal Intestine Large	intestine
26	chr20:12998800-12999600	Weak transcription	Fetal Intestine Small	intestine
27	chr20:12999000-13000800	Strong transcription	HepG2	liver

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