Variant report

Variant	rs7645445
Chromosome Location	chr3:49502243-49502244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:49502233-49503281	HCT-116	colon:	n/a	chr3:49502814-49502825
2	CEBPB	chr3:49502230-49503324	HCT-116	colon:	n/a	chr3:49502814-49502825

No.	Distal block	Cell Line	Cell type
1	chr3:49449241..49451638-chr3:49500834..49502786,2	MCF-7	breast:
2	chr3:49496719..49502585-chr3:49503472..49509213,13	MCF-7	breast:
3	chr3:49501861..49505109-chr3:49505439..49508808,5	K562	blood:

Variant related genes	Relation type
DAG1	TF binding region
ENSG00000067560	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000201301	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1050088	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865955	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130192	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130194	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130196	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130199	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130202	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130206	0.85[EUR][1000 genomes]
rs11711485	0.90[ASN][1000 genomes]
rs11720264	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12488065	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12489092	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13079643	0.83[ASN][1000 genomes]
rs13096760	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1464566	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1568662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17595772	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17650792	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2117939	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2312461	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2878298	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34937635	0.84[EUR][1000 genomes]
rs35115732	0.83[ASN][1000 genomes]
rs35701831	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3870337	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3870338	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3877784	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3924462	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3924463	0.91[EUR][1000 genomes]
rs4241406	0.87[EUR][1000 genomes]
rs4241408	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4459909	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4563439	0.80[EUR][1000 genomes]
rs4855836	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855839	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4855842	0.87[EUR][1000 genomes]
rs4855843	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855855	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855859	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855861	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855864	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4855866	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855873	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955412	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55957735	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59152804	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62259939	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62259942	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62261185	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446274	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6446277	0.83[ASN][1000 genomes]
rs67216675	0.90[ASN][1000 genomes]
rs6773518	0.86[EUR][1000 genomes]
rs6784820	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792911	0.87[EUR][1000 genomes]
rs6797765	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71324962	0.83[ASN][1000 genomes]
rs7371895	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7373849	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7621003	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7631908	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7637665	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7637999	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7643586	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7643845	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7646366	0.83[ASN][1000 genomes]
rs885592	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841110	0.90[ASN][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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7645445	WDR6	cis	Whole Blood	GTEx
rs7645445	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs7645445	WDR6	cis	lung	GTEx
rs7645445	WDR6	cis	Nerve Tibial	GTEx
rs7645445	WDR6	cis	Artery Tibial	GTEx
rs7645445	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7645445	WDR6	cis	Adipose Subcutaneous	GTEx
rs7645445	WDR6	cis	Muscle Skeletal	GTEx
rs7645445	AMT	cis	Thyroid	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
2	chr3:49491800-49506200	Enhancers	Placenta	Placenta
3	chr3:49497400-49506400	Weak transcription	Brain Germinal Matrix	brain
4	chr3:49498000-49506000	Weak transcription	Fetal Stomach	stomach
5	chr3:49499600-49503000	Weak transcription	Colonic Mucosa	Colon
6	chr3:49499600-49503000	Weak transcription	Right Atrium	heart
7	chr3:49499600-49503000	Weak transcription	Spleen	Spleen
8	chr3:49499600-49503200	Weak transcription	Esophagus	oesophagus
9	chr3:49499600-49503200	Weak transcription	Lung	lung
10	chr3:49499600-49503200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:49499600-49506600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:49499800-49502600	Weak transcription	Fetal Heart	heart
13	chr3:49499800-49503000	Weak transcription	Right Ventricle	heart
14	chr3:49499800-49503000	Weak transcription	HMEC	breast
15	chr3:49500000-49502400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:49500000-49502400	Weak transcription	NHEK	skin
17	chr3:49500000-49502600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:49500000-49502800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:49500000-49502800	Weak transcription	Fetal Intestine Large	intestine
20	chr3:49500000-49502800	Weak transcription	Fetal Intestine Small	intestine
21	chr3:49500000-49503000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:49500000-49503000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49500000-49503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:49500000-49503000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:49500000-49503000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:49500000-49503000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:49500000-49503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:49500000-49503000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:49500000-49503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:49500000-49503000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:49500000-49503000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:49500000-49503000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:49500000-49503000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:49500000-49503000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:49500000-49503000	Weak transcription	Gastric	stomach
36	chr3:49500000-49503000	Weak transcription	Left Ventricle	heart
37	chr3:49500000-49503000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:49500000-49503000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:49500000-49503000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:49500000-49503000	Weak transcription	Stomach Mucosa	stomach
41	chr3:49500000-49503000	Weak transcription	A549	lung
42	chr3:49500000-49503000	Weak transcription	HSMM	muscle
43	chr3:49500000-49503000	Weak transcription	HSMMtube	muscle
44	chr3:49500000-49503400	Weak transcription	Small Intestine	intestine
45	chr3:49500000-49504800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:49500000-49505600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:49500000-49505600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:49500000-49506200	Weak transcription	Adipose Nuclei	Adipose
49	chr3:49500000-49506400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:49500000-49506400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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