Variant report

Variant	rs6033633
Chromosome Location	chr20:13141809-13141810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11908677	1.00[EUR][1000 genomes]
rs1321254	1.00[EUR][1000 genomes]
rs1321255	1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[EUR][1000 genomes]
rs3747936	1.00[ASN][1000 genomes]
rs41275398	1.00[ASN][1000 genomes]
rs57130258	1.00[ASN][1000 genomes]
rs57622246	1.00[ASN][1000 genomes]
rs57995190	1.00[ASN][1000 genomes]
rs58478430	1.00[ASN][1000 genomes]
rs6033626	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6033632	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041913	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6041922	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6041925	1.00[ASN][1000 genomes]
rs6041926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041928	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041929	1.00[ASN][1000 genomes]
rs6041930	1.00[ASN][1000 genomes]
rs6041931	1.00[ASN][1000 genomes]
rs6041932	1.00[ASN][1000 genomes]
rs6041933	1.00[ASN][1000 genomes]
rs6041935	1.00[ASN][1000 genomes]
rs6041936	1.00[ASN][1000 genomes]
rs6041939	1.00[ASN][1000 genomes]
rs6041940	1.00[ASN][1000 genomes]
rs6109697	1.00[MEX][hapmap]
rs61496996	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	nsv912685	chr20:13134768-13234124	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6033633	RIN2	trans	lymphoblastoid	seeQTL
rs6033633	CCL20	trans	lymphoblastoid	seeQTL
rs6033633	SLC22A23	trans	lymphoblastoid	seeQTL
rs6033633	GPM6A	trans	lymphoblastoid	seeQTL
rs6033633	GLT25D2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13093000-13144600	Weak transcription	Pancreas	Pancrea
2	chr20:13108200-13145000	Weak transcription	Gastric	stomach
3	chr20:13111200-13144000	Weak transcription	Thymus	Thymus
4	chr20:13114200-13149200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr20:13115600-13143400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:13128000-13148400	Weak transcription	Left Ventricle	heart
7	chr20:13128800-13142400	Weak transcription	Fetal Kidney	kidney
8	chr20:13128800-13144000	Weak transcription	Fetal Stomach	stomach
9	chr20:13129400-13148200	Strong transcription	Placenta	Placenta
10	chr20:13129400-13148800	Weak transcription	Fetal Lung	lung
11	chr20:13129600-13144800	Weak transcription	Lung	lung
12	chr20:13131200-13144000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr20:13132800-13148000	Weak transcription	Primary T cells from cord blood	blood
14	chr20:13133800-13146800	Strong transcription	Liver	Liver
15	chr20:13135800-13151800	Weak transcription	Fetal Intestine Small	intestine
16	chr20:13136400-13147400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:13139000-13143400	Strong transcription	HepG2	liver
18	chr20:13139600-13143200	Weak transcription	Fetal Muscle Leg	muscle
19	chr20:13139800-13144200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr20:13139800-13145000	Weak transcription	Aorta	Aorta
21	chr20:13139800-13145600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr20:13140000-13143600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr20:13140000-13148000	Weak transcription	Adipose Nuclei	Adipose
24	chr20:13140200-13148800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr20:13140600-13143400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr20:13140600-13143800	Strong transcription	Fetal Intestine Large	intestine
27	chr20:13140800-13143200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:13140800-13143400	Strong transcription	Ovary	ovary
29	chr20:13141000-13142400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:13141000-13142400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr20:13141400-13142600	Enhancers	Fetal Brain Male	brain
32	chr20:13141600-13144400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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