Variant report

Variant	rs2227891
Chromosome Location	chr20:25262769-25262770
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25260536..25263156-chr20:25267514..25269055,2	MCF-7	breast:
2	chr20:25261291..25263117-chr20:25263430..25265103,2	MCF-7	breast:
3	chr20:25258137..25259676-chr20:25261708..25264458,2	K562	blood:
4	chr20:25252960..25255983-chr20:25260897..25264213,3	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11087508	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2072975	1.00[ASW][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2179638	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2228976	0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235605	1.00[ASW][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap]
rs2235606	0.80[JPT][hapmap]
rs2235607	0.81[JPT][hapmap]
rs2236180	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2254046	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2257370	0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2258052	0.86[EUR][1000 genomes]
rs2258053	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2261177	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2263205	0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2281559	1.00[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424701	1.00[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424707	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2424709	0.86[EUR][1000 genomes]
rs2482908	0.81[ASN][1000 genomes]
rs2482933	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2482934	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2482938	0.82[ASN][1000 genomes]
rs2482947	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2500395	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2500403	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2500441	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2500442	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3787078	1.00[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787081	1.00[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6050603	0.83[AMR][1000 genomes]
rs6138569	1.00[ASW][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes]
rs753009	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8116542	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2227891	PYGB	cis	Whole Blood	GTEx
rs2227891	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs2227891	C20orf22	cis	multi-tissue	Pritchard
rs2227891	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs2227891	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs2227891	PYGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25237600-25262800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:25241800-25273200	Weak transcription	Stomach Mucosa	stomach
5	chr20:25243000-25269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:25249200-25274800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:25249200-25275000	Strong transcription	A549	lung
10	chr20:25249200-25285800	Strong transcription	Dnd41	blood
11	chr20:25249400-25274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr20:25249400-25274800	Strong transcription	Osteobl	bone
13	chr20:25249400-25276200	Strong transcription	Fetal Intestine Large	intestine
14	chr20:25249600-25267000	Strong transcription	NH-A	brain
15	chr20:25249600-25273400	Strong transcription	NHEK	skin
16	chr20:25249600-25274400	Strong transcription	Lung	lung
17	chr20:25249600-25274600	Strong transcription	Primary T cells from cord blood	blood
18	chr20:25249600-25274600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr20:25249600-25274800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr20:25249600-25275000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr20:25249600-25275000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr20:25249600-25275000	Strong transcription	NHLF	lung
23	chr20:25249600-25275200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr20:25249800-25264800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr20:25249800-25270000	Strong transcription	Aorta	Aorta
30	chr20:25249800-25273200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr20:25249800-25273400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr20:25249800-25273400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr20:25249800-25274000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr20:25249800-25274600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr20:25249800-25274600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr20:25249800-25275000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr20:25249800-25275200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr20:25249800-25275200	Strong transcription	Fetal Stomach	stomach
39	chr20:25249800-25276400	Strong transcription	Fetal Intestine Small	intestine
40	chr20:25249800-25284400	Strong transcription	Brain Germinal Matrix	brain
41	chr20:25250000-25269600	Strong transcription	Placenta	Placenta
42	chr20:25250000-25273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr20:25250000-25274800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr20:25250000-25274800	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr20:25250000-25275800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr20:25250200-25266600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr20:25250600-25276200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr20:25250800-25285000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr20:25251400-25275400	Strong transcription	Thymus	Thymus
50	chr20:25251800-25268600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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