Variant report

Variant	rs56004653
Chromosome Location	chr3:49072228-49072229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49071967..49073878-chr3:49128851..49131278,2	K562	blood:

Variant related genes	Relation type
ENSG00000198218	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11552724	0.81[AMR][1000 genomes]
rs11706052	0.88[AMR][1000 genomes]
rs11712006	0.88[AMR][1000 genomes]
rs11716614	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11718982	0.88[AMR][1000 genomes]
rs13072554	0.88[AMR][1000 genomes]
rs13080725	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13086240	0.81[AMR][1000 genomes]
rs34504524	0.88[AMR][1000 genomes]
rs34580506	0.88[AMR][1000 genomes]
rs34889065	0.81[AMR][1000 genomes]
rs35102816	0.88[AMR][1000 genomes]
rs35108630	0.88[AMR][1000 genomes]
rs35283189	0.88[AMR][1000 genomes]
rs35673421	0.81[AMR][1000 genomes]
rs3923475	0.88[AMR][1000 genomes]
rs5030795	0.81[AMR][1000 genomes]
rs55921200	0.88[AMR][1000 genomes]
rs61729488	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71324929	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73080312	0.87[AMR][1000 genomes]
rs73080361	0.84[AMR][1000 genomes]
rs73082362	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs56004653	WDR6	cis	Whole Blood	GTEx
rs56004653	WDR6	cis	Adipose Subcutaneous	GTEx
rs56004653	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs56004653	WDR6	cis	Esophagus Mucosa	GTEx
rs56004653	USP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49067000-49074200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:49067200-49074800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:49067200-49078600	Weak transcription	Psoas Muscle	Psoas
6	chr3:49067200-49085600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
8	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:49067400-49072400	Strong transcription	Spleen	Spleen
10	chr3:49067400-49072600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49067400-49073200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr3:49067400-49073600	Strong transcription	HUVEC	blood vessel
13	chr3:49067400-49074000	Strong transcription	NHDF-Ad	bronchial
14	chr3:49067400-49074800	Strong transcription	Hela-S3	cervix
15	chr3:49067400-49075000	Strong transcription	HepG2	liver
16	chr3:49067400-49075400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:49067400-49075400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:49067400-49075600	Strong transcription	NHEK	skin
19	chr3:49067400-49076400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:49067400-49077200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:49067400-49079800	Strong transcription	Placenta	Placenta
22	chr3:49067400-49085000	Strong transcription	Brain Germinal Matrix	brain
23	chr3:49067400-49085600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr3:49067400-49085600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:49067400-49085600	Strong transcription	Fetal Intestine Large	intestine
26	chr3:49067400-49086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:49067400-49086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:49067400-49090000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
32	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
33	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
34	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:49067600-49072400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr3:49067600-49072400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:49067600-49072600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr3:49067600-49073600	Strong transcription	Fetal Brain Female	brain
40	chr3:49067600-49074200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:49067600-49074200	Strong transcription	GM12878-XiMat	blood
42	chr3:49067600-49074400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:49067600-49074400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:49067600-49074600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr3:49067600-49075400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:49067600-49080200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:49067600-49085600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:49067600-49085600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:49067600-49085600	Strong transcription	Liver	Liver
50	chr3:49067600-49086600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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