Variant report

Variant	rs17812197
Chromosome Location	chr20:13110632-13110633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1407332	0.81[EUR][1000 genomes]
rs17226481	0.81[EUR][1000 genomes]
rs55714827	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55737114	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56017021	0.81[EUR][1000 genomes]
rs56020710	0.81[EUR][1000 genomes]
rs73085884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73085885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73085887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73085888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73085892	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73085895	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73087703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73087773	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73087783	0.81[EUR][1000 genomes]
rs73087794	0.81[EUR][1000 genomes]
rs73087799	0.81[EUR][1000 genomes]
rs73087802	0.81[EUR][1000 genomes]
rs73089505	0.81[EUR][1000 genomes]
rs73089506	0.81[EUR][1000 genomes]
rs73089521	0.81[EUR][1000 genomes]
rs73089525	0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17812197	TMPRSS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:34 , 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	chr20:13083600-13114600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr20:13086600-13123200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:13091800-13127800	Weak transcription	Fetal Kidney	kidney
6	chr20:13093000-13144600	Weak transcription	Pancreas	Pancrea
7	chr20:13093400-13111000	Weak transcription	Lung	lung
8	chr20:13094600-13114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:13096600-13116600	Weak transcription	Right Ventricle	heart
10	chr20:13101000-13110800	Weak transcription	Small Intestine	intestine
11	chr20:13101600-13113600	Weak transcription	Fetal Stomach	stomach
12	chr20:13102000-13112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:13102200-13111000	Strong transcription	Placenta	Placenta
14	chr20:13103800-13118600	Strong transcription	Fetal Intestine Large	intestine
15	chr20:13105000-13113600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr20:13108200-13113400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:13108200-13145000	Weak transcription	Gastric	stomach
18	chr20:13108600-13116800	Weak transcription	NHEK	skin
19	chr20:13109000-13112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:13109000-13118800	Weak transcription	Esophagus	oesophagus
21	chr20:13109200-13110800	Weak transcription	Aorta	Aorta
22	chr20:13109200-13111000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr20:13109200-13113600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr20:13109200-13115600	Weak transcription	Fetal Lung	lung
25	chr20:13109200-13116800	Strong transcription	Liver	Liver
26	chr20:13109400-13112200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr20:13109400-13114400	Weak transcription	Ovary	ovary
28	chr20:13109400-13114800	Strong transcription	Fetal Intestine Small	intestine
29	chr20:13109400-13122000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:13109400-13122200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr20:13109400-13128000	Weak transcription	Adipose Nuclei	Adipose
32	chr20:13109600-13116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr20:13109800-13111800	Genic enhancers	HepG2	liver
34	chr20:13110000-13126400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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