Variant report

Variant	rs467912
Chromosome Location	chr22:29942252-29942253
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29942131..29944631-chr22:29945594..29947597,2	MCF-7	breast:
2	chr22:29873715..29877046-chr22:29940798..29944268,3	K562	blood:

Variant related genes	Relation type
ENSG00000100285	Chromatin interaction
ENSG00000225465	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10427559	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10427614	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10427824	0.96[ASN][1000 genomes]
rs1049534	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11704049	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12628784	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2074948	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2074951	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2188120	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2240637	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262240	0.84[EUR][1000 genomes]
rs2302141	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs425992	0.80[EUR][1000 genomes]
rs433194	0.83[EUR][1000 genomes]
rs457295	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457335	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459351	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459450	0.83[EUR][1000 genomes]
rs460428	0.85[EUR][1000 genomes]
rs4608625	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs460994	0.83[EUR][1000 genomes]
rs462444	0.85[EUR][1000 genomes]
rs467555	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs467902	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468019	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468224	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs468356	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs468475	0.91[EUR][1000 genomes]
rs468692	0.91[EUR][1000 genomes]
rs469230	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs469253	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs469295	0.85[EUR][1000 genomes]
rs469363	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs469565	0.84[EUR][1000 genomes]
rs55652051	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs55752411	0.80[ASN][1000 genomes]
rs56166672	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752937	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs5752940	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5763292	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs5763293	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs5763297	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763300	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763301	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763303	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763305	0.98[ASN][1000 genomes]
rs5763306	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57995869	0.98[ASN][1000 genomes]
rs695525	0.85[EUR][1000 genomes]
rs695780	0.89[EUR][1000 genomes]
rs695816	0.85[EUR][1000 genomes]
rs73159006	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7609	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8135828	0.97[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
rs467912	THOC5	cis	Artery Tibial	GTEx
rs467912	THOC5	cis	Muscle Skeletal	GTEx
rs467912	THOC5	cis	Esophagus Muscularis	GTEx
rs467912	THOC5	cis	lung	GTEx
rs467912	THOC5	cis	Nerve Tibial	GTEx
rs467912	THOC5	cis	Artery Aorta	GTEx
rs467912	THOC5	cis	Thyroid	GTEx
rs467912	THOC5	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr22:29911200-29947000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr22:29911400-29945400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
12	chr22:29917800-29942400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:29918000-29948000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr22:29919000-29946600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr22:29919200-29946600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr22:29919200-29946800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr22:29919400-29942400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr22:29919400-29942400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr22:29919400-29942400	Strong transcription	Osteobl	bone
20	chr22:29919400-29945200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr22:29919400-29946200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr22:29919400-29946600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr22:29919400-29946800	Strong transcription	Fetal Muscle Leg	muscle
24	chr22:29919400-29947000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr22:29919400-29947000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr22:29919600-29945400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr22:29919600-29945400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:29919800-29945800	Strong transcription	Thymus	Thymus
29	chr22:29921000-29945400	Strong transcription	Liver	Liver
30	chr22:29925000-29949200	Weak transcription	Small Intestine	intestine
31	chr22:29925600-29946600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr22:29925800-29947000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr22:29925800-29948800	Weak transcription	Stomach Mucosa	stomach
34	chr22:29928000-29947400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr22:29929200-29945400	Strong transcription	Left Ventricle	heart
36	chr22:29929400-29945400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr22:29930200-29948800	Weak transcription	Fetal Heart	heart
38	chr22:29930400-29943000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr22:29930400-29946800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr22:29930400-29947000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr22:29930400-29947000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr22:29930600-29947800	Strong transcription	Fetal Intestine Small	intestine
43	chr22:29930600-29947800	Strong transcription	Fetal Stomach	stomach
44	chr22:29930800-29947800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:29931200-29945400	Strong transcription	Lung	lung
46	chr22:29931400-29946800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr22:29931600-29945800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr22:29931600-29946600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr22:29931600-29946800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr22:29931800-29942400	Strong transcription	Right Ventricle	heart

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