Variant report

Variant	rs165668
Chromosome Location	chr22:29890403-29890404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29877857..29880129-chr22:29887823..29890747,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11704899	0.85[ASN][1000 genomes]
rs165625	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs165663	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs165743	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs165803	0.83[EUR][1000 genomes]
rs165894	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs174650	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs174651	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074951	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2188120	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55652051	0.94[ASN][1000 genomes]
rs5752930	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5752933	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752937	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763269	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763275	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5763276	0.92[EUR][1000 genomes]
rs5763286	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763287	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763292	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763293	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8137532	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8140848	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs165668	THOC5	cis	Nerve Tibial	GTEx
rs165668	THOC5	cis	Muscle Skeletal	GTEx
rs165668	THOC5	cis	Thyroid	GTEx
rs165668	THOC5	cis	lung	GTEx
rs165668	THOC5	cis	Artery Tibial	GTEx
rs165668	THOC5	cis	Artery Aorta	GTEx
rs165668	THOC5	cis	Adipose Subcutaneous	GTEx
rs165668	THOC5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29877400-29900600	Weak transcription	Right Atrium	heart
2	chr22:29878000-29900800	Weak transcription	Fetal Brain Female	brain
3	chr22:29878000-29903000	Weak transcription	Pancreas	Pancrea
4	chr22:29878400-29895600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:29878400-29899800	Weak transcription	Fetal Intestine Large	intestine
6	chr22:29878400-29899800	Weak transcription	NH-A	brain
7	chr22:29878600-29890600	Weak transcription	HSMM	muscle
8	chr22:29878800-29890600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr22:29878800-29902600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:29879000-29890600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr22:29879000-29898600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr22:29879000-29899600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr22:29879200-29890600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr22:29879200-29901200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr22:29879600-29898800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr22:29879600-29899400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr22:29880200-29890600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:29880400-29901000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:29882000-29899200	Weak transcription	Brain Angular Gyrus	brain
20	chr22:29882600-29890600	Weak transcription	Fetal Intestine Small	intestine
21	chr22:29882800-29903200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr22:29883400-29890600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr22:29883400-29890600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:29883600-29899800	Weak transcription	Brain Germinal Matrix	brain
25	chr22:29883800-29904000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:29884000-29902200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr22:29884800-29901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr22:29885000-29902600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr22:29885400-29890600	Weak transcription	Spleen	Spleen
30	chr22:29885600-29890600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr22:29885600-29904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:29886000-29903400	Weak transcription	Gastric	stomach
33	chr22:29886200-29895400	Weak transcription	Fetal Stomach	stomach
34	chr22:29886200-29899600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr22:29886200-29902800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr22:29886800-29899800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr22:29887400-29890600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr22:29887400-29902000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr22:29887600-29902000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr22:29888000-29890600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr22:29888800-29901000	Weak transcription	Thymus	Thymus
42	chr22:29888800-29901200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr22:29889000-29890600	Weak transcription	Fetal Lung	lung
44	chr22:29889000-29900800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr22:29889200-29890600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr22:29889200-29890600	Weak transcription	Adipose Nuclei	Adipose
47	chr22:29889400-29899800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr22:29889600-29899800	Weak transcription	NHLF	lung
49	chr22:29889800-29899800	Weak transcription	NHDF-Ad	bronchial
50	chr22:29890000-29890600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links