Variant report

Variant	rs3787573
Chromosome Location	chr20:1100669-1100670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1099609..1102022-chr20:1115738..1118219,2	K562	blood:
2	chr20:1099357..1100931-chr20:1102003..1104319,2	K562	blood:
3	chr20:1099416..1102293-chr20:1159326..1161396,2	K562	blood:
4	chr20:1099167..1103189-chr20:1144544..1147545,4	K562	blood:

Variant related genes	Relation type
ENSG00000125818	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11087015	1.00[ASN][1000 genomes]
rs11696399	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11696575	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11696674	0.91[EUR][1000 genomes]
rs11697070	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11699188	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11699627	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11699981	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs45443791	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4553882	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6032877	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6032895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6032947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6039915	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6039922	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6039940	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6040044	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60728448	1.00[ASN][1000 genomes]
rs6514113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514115	0.84[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];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73071630	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7348188	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8117499	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1055328	chr20:867911-1145765	Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
9	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv949356	chr20:961527-1135413	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv1799982	chr20:1097289-1136252	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3787573	PSMF1	cis	Artery Tibial	GTEx
rs3787573	PSMF1	cis	Esophagus Muscularis	GTEx
rs3787573	PSMF1	cis	Nerve Tibial	GTEx
rs3787573	PSMF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1098400-1101000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr20:1099000-1101000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr20:1099400-1100800	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr20:1099400-1100800	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr20:1099400-1101600	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr20:1099600-1100800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr20:1099600-1101000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:1099600-1101000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr20:1099600-1101200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:1099800-1100800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:1099800-1100800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr20:1099800-1100800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr20:1099800-1100800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr20:1099800-1100800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr20:1099800-1100800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr20:1099800-1100800	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr20:1099800-1100800	Flanking Active TSS	Fetal Heart	heart
18	chr20:1099800-1100800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr20:1099800-1101000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr20:1099800-1101000	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr20:1099800-1101000	Flanking Active TSS	Fetal Lung	lung
22	chr20:1099800-1101000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr20:1099800-1101000	Flanking Active TSS	Hela-S3	cervix
24	chr20:1099800-1101200	Flanking Active TSS	Fetal Brain Female	brain
25	chr20:1099800-1101600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr20:1100000-1100800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr20:1100000-1100800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr20:1100000-1101000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr20:1100000-1101000	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr20:1100000-1101000	Flanking Active TSS	HMEC	breast
31	chr20:1100000-1101200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr20:1100200-1100800	Flanking Active TSS	Fetal Kidney	kidney
33	chr20:1100200-1100800	Enhancers	Spleen	Spleen
34	chr20:1100200-1100800	Flanking Active TSS	GM12878-XiMat	blood
35	chr20:1100200-1100800	Flanking Active TSS	NHEK	skin
36	chr20:1100200-1101000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr20:1100200-1101200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr20:1100200-1101200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr20:1100200-1101200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:1100200-1101400	Enhancers	Small Intestine	intestine
41	chr20:1100200-1101600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr20:1100200-1105800	Weak transcription	Aorta	Aorta
43	chr20:1100200-1106200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:1100400-1100800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr20:1100400-1100800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr20:1100400-1101000	Enhancers	Brain Angular Gyrus	brain
47	chr20:1100400-1101000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr20:1100400-1101000	Enhancers	Fetal Brain Male	brain
49	chr20:1100400-1101000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
50	chr20:1100400-1101000	Enhancers	Ovary	ovary

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