Variant report

Variant	rs469565
Chromosome Location	chr22:29952437-29952438
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	POLR2A	chr22:29952339-29952469	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29951234..29953501-chr22:29974521..29977004,2	MCF-7	breast:

Variant related genes	Relation type
THOC5	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1049534	0.82[EUR][1000 genomes]
rs11705569	0.81[ASN][1000 genomes]
rs12628784	0.81[EUR][1000 genomes]
rs16987832	0.85[ASN][1000 genomes]
rs16987839	0.82[ASN][1000 genomes]
rs2074948	0.82[EUR][1000 genomes]
rs2240637	0.84[EUR][1000 genomes]
rs2262240	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2302141	0.81[EUR][1000 genomes]
rs2530656	0.84[ASN][1000 genomes]
rs2530658	0.81[ASN][1000 genomes]
rs425992	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs433194	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs456585	0.90[ASN][1000 genomes]
rs457295	0.85[EUR][1000 genomes]
rs457335	0.84[EUR][1000 genomes]
rs458196	0.85[ASN][1000 genomes]
rs459351	0.84[EUR][1000 genomes]
rs459450	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs460428	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4608625	0.82[EUR][1000 genomes]
rs460994	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs462444	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs463220	0.86[ASN][1000 genomes]
rs467902	0.85[EUR][1000 genomes]
rs467912	0.84[EUR][1000 genomes]
rs468019	0.86[EUR][1000 genomes]
rs468224	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468254	0.90[ASN][1000 genomes]
rs468356	0.84[EUR][1000 genomes]
rs468475	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs468692	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs468795	0.95[ASN][1000 genomes]
rs468852	0.90[ASN][1000 genomes]
rs469230	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469253	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469295	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs469363	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752940	0.84[EUR][1000 genomes]
rs5763297	0.80[EUR][1000 genomes]
rs5763300	0.82[EUR][1000 genomes]
rs5763301	0.84[EUR][1000 genomes]
rs5763303	0.84[EUR][1000 genomes]
rs5763306	0.84[EUR][1000 genomes]
rs695525	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs695780	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs695816	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73159006	0.82[EUR][1000 genomes]
rs73159040	0.81[ASN][1000 genomes]
rs7609	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8141518	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs469565	THOC5	cis	Adipose Subcutaneous	GTEx
rs469565	THOC5	cis	Thyroid	GTEx
rs469565	THOC5	cis	Esophagus Muscularis	GTEx
rs469565	THOC5	cis	Muscle Skeletal	GTEx
rs469565	THOC5	cis	Artery Aorta	GTEx
rs469565	THOC5	cis	lung	GTEx
rs469565	THOC5	cis	Artery Tibial	GTEx
rs469565	THOC5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29950200-29953800	Weak transcription	Esophagus	oesophagus
2	chr22:29950200-29976000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:29950400-29953600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr22:29950400-29953600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr22:29950400-29953600	Weak transcription	Aorta	Aorta
6	chr22:29950400-29953600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr22:29950400-29953600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr22:29950400-29954200	Weak transcription	HSMM	muscle
9	chr22:29950400-29954400	Weak transcription	K562	blood
10	chr22:29950400-29954800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr22:29950400-29957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr22:29950400-29965200	Weak transcription	Small Intestine	intestine
13	chr22:29950400-29976200	Weak transcription	HMEC	breast
14	chr22:29950600-29952600	Weak transcription	Primary B cells from cord blood	blood
15	chr22:29950600-29953400	Weak transcription	Colon Smooth Muscle	Colon
16	chr22:29950600-29953600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr22:29950600-29953600	Weak transcription	NHEK	skin
18	chr22:29950600-29953800	Weak transcription	Stomach Mucosa	stomach
19	chr22:29950600-29957000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:29950600-29958400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:29950600-29962200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr22:29950600-29964800	Strong transcription	Fetal Intestine Large	intestine
23	chr22:29950600-29964800	Strong transcription	Fetal Intestine Small	intestine
24	chr22:29950600-29967400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr22:29950600-29967600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr22:29950600-29968000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr22:29950600-29971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:29950800-29953600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr22:29950800-29953600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr22:29950800-29953600	Weak transcription	Adipose Nuclei	Adipose
31	chr22:29950800-29953600	Weak transcription	Fetal Brain Male	brain
32	chr22:29950800-29953800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr22:29950800-29956600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr22:29950800-29958400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr22:29950800-29958400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr22:29950800-29958400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr22:29950800-29958600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr22:29950800-29958800	Strong transcription	Fetal Brain Female	brain
39	chr22:29950800-29959200	Weak transcription	Hela-S3	cervix
40	chr22:29950800-29959600	Weak transcription	Fetal Heart	heart
41	chr22:29950800-29959600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr22:29950800-29961600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr22:29950800-29966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr22:29950800-29966800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr22:29950800-29967000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr22:29950800-29976200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr22:29951000-29952800	Strong transcription	NHLF	lung
48	chr22:29951000-29953000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr22:29951000-29953000	Weak transcription	Pancreas	Pancrea
50	chr22:29951000-29953000	Weak transcription	Rectal Smooth Muscle	rectum

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