Variant report

Variant	rs6041885
Chromosome Location	chr20:13107970-13107971
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1052038	0.85[ASN][1000 genomes]
rs2073303	0.83[JPT][hapmap]
rs2144134	0.86[ASN][1000 genomes]
rs4431013	0.88[JPT][hapmap]
rs4813116	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033623	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6033625	0.88[JPT][hapmap]
rs6041890	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6041897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6041937	0.83[ASN][1000 genomes]
rs6078937	0.83[JPT][hapmap]
rs6105044	0.88[JPT][hapmap]

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	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
14	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13049600-13121800	Weak transcription	Primary T cells from cord blood	blood
2	chr20:13049800-13117600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:13071600-13108000	Weak transcription	Left Ventricle	heart
4	chr20:13083600-13114600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:13086600-13123200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:13087000-13108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:13091800-13127800	Weak transcription	Fetal Kidney	kidney
8	chr20:13093000-13144600	Weak transcription	Pancreas	Pancrea
9	chr20:13093400-13108000	Weak transcription	Aorta	Aorta
10	chr20:13093400-13111000	Weak transcription	Lung	lung
11	chr20:13094600-13114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:13096600-13116600	Weak transcription	Right Ventricle	heart
13	chr20:13100000-13108800	Weak transcription	Adipose Nuclei	Adipose
14	chr20:13101000-13110800	Weak transcription	Small Intestine	intestine
15	chr20:13101600-13113600	Weak transcription	Fetal Stomach	stomach
16	chr20:13102000-13112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr20:13102200-13108400	Strong transcription	Liver	Liver
18	chr20:13102200-13111000	Strong transcription	Placenta	Placenta
19	chr20:13103200-13108800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr20:13103200-13109800	Weak transcription	Colonic Mucosa	Colon
21	chr20:13103600-13108400	Strong transcription	HepG2	liver
22	chr20:13103800-13118600	Strong transcription	Fetal Intestine Large	intestine
23	chr20:13104200-13109200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr20:13105000-13113600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr20:13106400-13108400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr20:13106800-13109400	Strong transcription	Ovary	ovary
27	chr20:13107200-13108200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:13107200-13108600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr20:13107200-13108800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr20:13107400-13108600	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr20:13107600-13108600	Strong transcription	NHEK	skin
32	chr20:13107800-13109400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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