Variant report

Variant	rs2873522
Chromosome Location	chr20:1419526-1419527
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1418412..1420201-chr20:1482742..1485316,2	K562	blood:
2	chr20:1413774..1421620-chr20:1445657..1450800,12	K562	blood:
3	chr20:1418150..1421031-chr20:1445969..1448576,3	MCF-7	breast:
4	chr20:1418037..1419774-chr20:1420141..1424100,3	MCF-7	breast:
5	chr20:1418229..1420990-chr20:1423275..1425647,2	MCF-7	breast:
6	chr20:1417607..1420469-chr20:1423578..1425297,2	K562	blood:
7	chr20:1419111..1421909-chr20:1426787..1429297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11696447	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11699494	1.00[CHB][hapmap]
rs12481707	1.00[JPT][hapmap]
rs13163	1.00[CHB][hapmap]
rs1474879	1.00[ASN][1000 genomes]
rs1474880	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap]
rs16995310	1.00[CHB][hapmap]
rs16995332	1.00[CHB][hapmap]
rs17793360	1.00[JPT][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884393	1.00[JPT][hapmap]
rs2064645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2273321	1.00[JPT][hapmap]
rs3829697	1.00[JPT][hapmap]
rs41308086	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs58194712	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042506	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042574	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105437	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109522	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109837	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109986	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110189	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110193	1.00[CHB][hapmap]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs66497853	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8117563	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8118276	1.00[CHB][hapmap]
rs8118710	1.00[JPT][hapmap]
rs8124855	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]
rs959813	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984497	1.00[JPT][hapmap]
rs984498	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2873522	DPYD	trans	lymphoblastoid	seeQTL
rs2873522	CDS2	cis	cerebellum	SCAN
rs2873522	TCF15	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
5	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
6	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
7	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
12	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
13	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
14	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr20:1411000-1419600	Weak transcription	Fetal Intestine Large	intestine
16	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
17	chr20:1411200-1420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr20:1411200-1420600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:1411800-1420400	Weak transcription	Aorta	Aorta
21	chr20:1412800-1420200	Weak transcription	Ovary	ovary
22	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
23	chr20:1413800-1420400	Weak transcription	Gastric	stomach
24	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
25	chr20:1414600-1419600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr20:1415200-1420200	Weak transcription	Pancreas	Pancrea
27	chr20:1415200-1422800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr20:1415400-1419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr20:1415400-1420400	Weak transcription	Fetal Lung	lung
30	chr20:1415400-1421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr20:1415400-1422400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr20:1415400-1422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr20:1415600-1420000	Weak transcription	Fetal Brain Female	brain
34	chr20:1415600-1420400	Weak transcription	A549	lung
35	chr20:1415600-1422600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr20:1415600-1423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr20:1415800-1419600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr20:1415800-1420600	Weak transcription	Brain Substantia Nigra	brain
39	chr20:1415800-1422000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:1416000-1420000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr20:1416000-1420200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr20:1416000-1420200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr20:1416000-1420200	Weak transcription	Adipose Nuclei	Adipose
44	chr20:1416000-1420400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:1416000-1420600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr20:1416000-1421000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr20:1416000-1421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr20:1416000-1421600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr20:1416000-1422000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:1416000-1422000	Weak transcription	HSMM	muscle

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