Variant report

Variant	rs2236124
Chromosome Location	chr20:13106725-13106726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11547796	0.85[AMR][1000 genomes]
rs11698429	1.00[ASW][hapmap]
rs17190927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17812209	0.83[AMR][1000 genomes]
rs3761896	1.00[ASW][hapmap]
rs6074564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[GIH][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6078931	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6078936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6078938	1.00[CHB][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6078946	0.85[AMR][1000 genomes]
rs6078948	0.85[AMR][1000 genomes]
rs6109723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67718002	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7264061	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap]
rs73610452	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73610453	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8119743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8121193	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2236124	NCRNA00029	trans	parietal	SCAN
rs2236124	GLYR1	trans	cerebellum	SCAN

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	chr20:13086200-13107600	Weak transcription	NHEK	skin
6	chr20:13086600-13123200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr20:13087000-13108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:13087800-13107200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr20:13091800-13127800	Weak transcription	Fetal Kidney	kidney
10	chr20:13093000-13144600	Weak transcription	Pancreas	Pancrea
11	chr20:13093200-13106800	Weak transcription	Ovary	ovary
12	chr20:13093400-13108000	Weak transcription	Aorta	Aorta
13	chr20:13093400-13111000	Weak transcription	Lung	lung
14	chr20:13094600-13114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:13096600-13116600	Weak transcription	Right Ventricle	heart
16	chr20:13098400-13107200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr20:13100000-13108800	Weak transcription	Adipose Nuclei	Adipose
18	chr20:13101000-13110800	Weak transcription	Small Intestine	intestine
19	chr20:13101600-13113600	Weak transcription	Fetal Stomach	stomach
20	chr20:13102000-13112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:13102200-13108400	Strong transcription	Liver	Liver
22	chr20:13102200-13111000	Strong transcription	Placenta	Placenta
23	chr20:13103200-13108800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr20:13103200-13109800	Weak transcription	Colonic Mucosa	Colon
25	chr20:13103600-13108400	Strong transcription	HepG2	liver
26	chr20:13103800-13118600	Strong transcription	Fetal Intestine Large	intestine
27	chr20:13104200-13109200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr20:13104600-13107200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr20:13105000-13113600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr20:13105200-13107800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr20:13106400-13107400	Weak transcription	Fetal Intestine Small	intestine
32	chr20:13106400-13108400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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