Variant report

Variant	rs468356
Chromosome Location	chr22:29947202-29947203
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:29947092-29947262	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29945702..29947218-chr22:29948273..29950145,2	MCF-7	breast:
2	chr22:29939607..29941990-chr22:29945256..29947722,2	MCF-7	breast:
3	chr22:29938209..29940408-chr22:29946980..29949798,2	K562	blood:
4	chr22:29935333..29937514-chr22:29945069..29947567,2	K562	blood:
5	chr22:29942131..29944631-chr22:29945594..29947597,2	MCF-7	breast:

No data

Variant related genes	Relation type
THOC5	TF binding region
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10427559	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10427614	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10427824	0.93[ASN][1000 genomes]
rs1049534	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11704049	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12628784	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074948	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074951	0.84[EUR][1000 genomes]
rs2188120	0.85[EUR][1000 genomes]
rs2240637	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2262240	0.84[EUR][1000 genomes]
rs2302141	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs425992	0.80[EUR][1000 genomes]
rs433194	0.83[EUR][1000 genomes]
rs457295	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs457335	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459351	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459450	0.83[EUR][1000 genomes]
rs460428	0.85[EUR][1000 genomes]
rs4608625	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs460994	0.83[EUR][1000 genomes]
rs462444	0.85[EUR][1000 genomes]
rs467555	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467902	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs467912	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs468019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468224	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs468475	0.90[EUR][1000 genomes]
rs468692	0.90[EUR][1000 genomes]
rs469230	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs469253	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs469295	0.85[EUR][1000 genomes]
rs469363	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs469565	0.84[EUR][1000 genomes]
rs55652051	0.82[EUR][1000 genomes]
rs56166672	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752937	0.85[EUR][1000 genomes]
rs5752940	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763292	0.84[EUR][1000 genomes]
rs5763293	0.84[EUR][1000 genomes]
rs5763297	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763300	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763301	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763303	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763305	0.95[ASN][1000 genomes]
rs5763306	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57995869	0.95[ASN][1000 genomes]
rs695525	0.85[EUR][1000 genomes]
rs695780	0.90[EUR][1000 genomes]
rs695816	0.85[EUR][1000 genomes]
rs73159006	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7609	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8135828	0.94[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
rs468356	THOC5	cis	Nerve Tibial	GTEx
rs468356	THOC5	cis	Adipose Subcutaneous	GTEx
rs468356	THOC5	cis	Artery Aorta	GTEx
rs468356	THOC5	cis	Muscle Skeletal	GTEx
rs468356	THOC5	cis	lung	GTEx
rs468356	THOC5	cis	Esophagus Muscularis	GTEx
rs468356	THOC5	cis	Thyroid	GTEx
rs468356	THOC5	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 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	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
8	chr22:29918000-29948000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:29925000-29949200	Weak transcription	Small Intestine	intestine
10	chr22:29925800-29948800	Weak transcription	Stomach Mucosa	stomach
11	chr22:29928000-29947400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr22:29930200-29948800	Weak transcription	Fetal Heart	heart
13	chr22:29930600-29947800	Strong transcription	Fetal Intestine Small	intestine
14	chr22:29930600-29947800	Strong transcription	Fetal Stomach	stomach
15	chr22:29930800-29947800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:29933000-29949000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr22:29933200-29949000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr22:29935800-29948600	Weak transcription	Fetal Brain Male	brain
19	chr22:29939600-29949200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:29940800-29949000	Weak transcription	NHDF-Ad	bronchial
21	chr22:29940800-29949200	Weak transcription	Psoas Muscle	Psoas
22	chr22:29943000-29948000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr22:29943200-29947600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr22:29944200-29947400	Strong transcription	Dnd41	blood
25	chr22:29944800-29949200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr22:29944800-29949200	Weak transcription	Colon Smooth Muscle	Colon
27	chr22:29945000-29948800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr22:29945000-29948800	Weak transcription	NHEK	skin
29	chr22:29945000-29949000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr22:29945000-29949200	Weak transcription	Ovary	ovary
31	chr22:29945000-29949200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr22:29945200-29948600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr22:29945200-29948600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr22:29945200-29948600	Weak transcription	Right Ventricle	heart
35	chr22:29945200-29948800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr22:29945200-29948800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr22:29945200-29948800	Weak transcription	Adipose Nuclei	Adipose
38	chr22:29945200-29948800	Weak transcription	Esophagus	oesophagus
39	chr22:29945200-29948800	Weak transcription	Placenta	Placenta
40	chr22:29945200-29948800	Weak transcription	HMEC	breast
41	chr22:29945200-29949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr22:29945200-29949000	Weak transcription	Colonic Mucosa	Colon
43	chr22:29945200-29949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr22:29945200-29949200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr22:29945200-29949200	Weak transcription	Brain Substantia Nigra	brain
46	chr22:29945200-29949200	Weak transcription	Pancreas	Pancrea
47	chr22:29945400-29948600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr22:29945400-29948600	Weak transcription	Liver	Liver
49	chr22:29945400-29948800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr22:29945400-29948800	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links