Variant report

Variant	rs3775839
Chromosome Location	chr4:119737885-119737886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119733532..119736191-chr4:119736876..119739551,2	K562	blood:
2	chr4:119737879..119739505-chr4:119745855..119747438,2	K562	blood:
3	chr4:119733774..119738029-chr4:119752570..119758602,5	K562	blood:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1019696	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11098453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098459	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11098460	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11722846	1.00[YRI][hapmap]
rs11931472	1.00[YRI][hapmap]
rs12512594	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12643205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13112913	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13139244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1365549	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1365550	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1365551	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1962840	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114461	0.81[ASN][1000 genomes]
rs2303512	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2389688	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34057511	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35934778	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36096663	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775840	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4833593	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4834704	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4834705	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4834706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811006	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6817084	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7375858	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv516777	chr4:119733366-119762951	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3775839	USP53	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119703800-119738200	Strong transcription	Placenta	Placenta
2	chr4:119704200-119740000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:119705200-119748200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:119712400-119739000	Strong transcription	Fetal Muscle Leg	muscle
5	chr4:119713800-119739600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr4:119714000-119738200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr4:119714000-119739000	Strong transcription	HSMM	muscle
8	chr4:119714000-119739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:119714400-119740200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:119716200-119738000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr4:119716800-119738600	Strong transcription	GM12878-XiMat	blood
12	chr4:119718200-119739600	Weak transcription	Brain Germinal Matrix	brain
13	chr4:119718400-119756000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:119718600-119744200	Weak transcription	Hela-S3	cervix
15	chr4:119718600-119753600	Weak transcription	Fetal Heart	heart
16	chr4:119719000-119756200	Weak transcription	Fetal Brain Male	brain
17	chr4:119720600-119738200	Strong transcription	NH-A	brain
18	chr4:119722800-119738600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:119723000-119738000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr4:119723200-119738600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:119723600-119738800	Strong transcription	Dnd41	blood
22	chr4:119724000-119748200	Weak transcription	Psoas Muscle	Psoas
23	chr4:119724600-119738200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:119725400-119738600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:119725400-119738600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:119725400-119739000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:119725600-119738600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:119725600-119738800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:119726200-119740000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:119727000-119744000	Weak transcription	Stomach Mucosa	stomach
31	chr4:119730400-119738200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:119730800-119739000	Strong transcription	HepG2	liver
33	chr4:119731000-119738800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:119732000-119748000	Weak transcription	Right Atrium	heart
35	chr4:119732000-119755800	Weak transcription	Brain Angular Gyrus	brain
36	chr4:119733200-119738000	Strong transcription	Rectal Smooth Muscle	rectum
37	chr4:119733400-119738600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:119733400-119738800	Strong transcription	HSMMtube	muscle
39	chr4:119733400-119740000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr4:119733400-119740400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:119733400-119753200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:119734400-119748200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:119734800-119755800	Weak transcription	Thymus	Thymus
44	chr4:119735000-119738600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:119735200-119738600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:119735400-119738800	Genic enhancers	NHLF	lung
47	chr4:119735400-119748200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:119735600-119738400	Strong transcription	Liver	Liver
49	chr4:119735600-119748200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:119735600-119748200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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