Variant report

Variant	rs468475
Chromosome Location	chr22:29958634-29958635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29953914..29956563-chr22:29957184..29959467,2	K562	blood:
2	chr22:29946832..29952460-chr22:29954697..29959036,10	MCF-7	breast:
3	chr22:29949399..29951085-chr22:29957518..29959930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10427559	0.86[EUR][1000 genomes]
rs10427614	0.86[EUR][1000 genomes]
rs1049534	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11704049	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11705569	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12628784	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16987832	0.86[ASN][1000 genomes]
rs16987839	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074948	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2188120	0.80[EUR][1000 genomes]
rs2240637	0.90[EUR][1000 genomes]
rs2262240	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302141	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2530656	0.84[ASN][1000 genomes]
rs2530658	0.82[ASN][1000 genomes]
rs425992	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs433194	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs456285	0.90[ASN][1000 genomes]
rs456585	0.91[ASN][1000 genomes]
rs457295	0.91[EUR][1000 genomes]
rs457335	0.90[EUR][1000 genomes]
rs458196	0.86[ASN][1000 genomes]
rs459351	0.90[EUR][1000 genomes]
rs459450	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460428	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4608625	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs460994	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs462444	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs463220	0.86[ASN][1000 genomes]
rs467555	0.86[EUR][1000 genomes]
rs467902	0.91[EUR][1000 genomes]
rs467912	0.91[EUR][1000 genomes]
rs468019	0.93[EUR][1000 genomes]
rs468224	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468254	0.91[ASN][1000 genomes]
rs468356	0.90[EUR][1000 genomes]
rs468692	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs468795	0.84[ASN][1000 genomes]
rs468852	0.91[ASN][1000 genomes]
rs469230	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs469253	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs469295	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469363	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs469565	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56166672	0.80[EUR][1000 genomes]
rs5752937	0.80[EUR][1000 genomes]
rs5752940	0.90[EUR][1000 genomes]
rs5763297	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs5763300	0.89[EUR][1000 genomes]
rs5763301	0.90[EUR][1000 genomes]
rs5763303	0.90[EUR][1000 genomes]
rs5763306	0.90[EUR][1000 genomes]
rs5763349	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs695525	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs695668	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs695780	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs695816	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73159006	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73159040	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7609	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8141518	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[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
rs468475	THOC5	cis	lung	GTEx
rs468475	THOC5	cis	Nerve Tibial	GTEx
rs468475	THOC5	cis	Artery Tibial	GTEx
rs468475	THOC5	cis	Artery Aorta	GTEx
rs468475	THOC5	cis	Thyroid	GTEx
rs468475	THOC5	cis	Adipose Subcutaneous	GTEx
rs468475	THOC5	cis	Muscle Skeletal	GTEx
rs468475	THOC5	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29950200-29976000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29950400-29965200	Weak transcription	Small Intestine	intestine
3	chr22:29950400-29976200	Weak transcription	HMEC	breast
4	chr22:29950600-29962200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr22:29950600-29964800	Strong transcription	Fetal Intestine Large	intestine
6	chr22:29950600-29964800	Strong transcription	Fetal Intestine Small	intestine
7	chr22:29950600-29967400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:29950600-29967600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr22:29950600-29968000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:29950600-29971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:29950800-29958800	Strong transcription	Fetal Brain Female	brain
12	chr22:29950800-29959200	Weak transcription	Hela-S3	cervix
13	chr22:29950800-29959600	Weak transcription	Fetal Heart	heart
14	chr22:29950800-29959600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr22:29950800-29961600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr22:29950800-29966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr22:29950800-29966800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr22:29950800-29967000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr22:29950800-29976200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr22:29951000-29960000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr22:29951000-29962000	Strong transcription	Thymus	Thymus
22	chr22:29951000-29966600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:29951000-29966800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr22:29951000-29967400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr22:29951000-29967400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr22:29951000-29967600	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr22:29951200-29958800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr22:29951200-29966400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:29951200-29967600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr22:29951200-29971400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:29951400-29958800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr22:29951400-29959000	Strong transcription	Brain Hippocampus Middle	brain
33	chr22:29951600-29971600	Strong transcription	Fetal Stomach	stomach
34	chr22:29951800-29959000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr22:29952000-29958800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr22:29952000-29958800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr22:29952000-29966600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr22:29952000-29976400	Weak transcription	Right Atrium	heart
39	chr22:29952200-29960000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr22:29952800-29964800	Weak transcription	HSMMtube	muscle
41	chr22:29953400-29960400	Strong transcription	Fetal Lung	lung
42	chr22:29953400-29966200	Strong transcription	Liver	Liver
43	chr22:29953600-29959800	Strong transcription	Lung	lung
44	chr22:29953600-29960800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr22:29953800-29958800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:29954200-29962200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr22:29955000-29959800	Weak transcription	Left Ventricle	heart
48	chr22:29955000-29976000	Weak transcription	NHEK	skin
49	chr22:29955200-29959600	Weak transcription	K562	blood
50	chr22:29955400-29964800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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