Variant report

Variant	rs28380
Chromosome Location	chr22:29866456-29866457
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29865160..29867687-chr22:29913906..29916895,2	MCF-7	breast:
2	chr22:29861087..29864747-chr22:29865747..29867984,3	K562	blood:
3	chr22:29792519..29794058-chr22:29864789..29867115,2	MCF-7	breast:
4	chr22:29866152..29869730-chr22:29872379..29875672,4	MCF-7	breast:
5	chr22:29866168..29866984-chr22:29877594..29878224,2	K562	blood:
6	chr22:29780492..29782846-chr22:29865528..29867159,2	MCF-7	breast:
7	chr22:29865857..29867643-chr22:29876448..29878393,2	MCF-7	breast:
8	chr22:29857259..29859794-chr22:29863672..29866457,2	K562	blood:
9	chr22:29863203..29869053-chr22:29871800..29876725,7	K562	blood:
10	chr22:29858816..29860851-chr22:29864972..29867318,2	MCF-7	breast:
11	chr22:29866353..29868086-chr22:29877604..29879531,2	K562	blood:
12	chr22:29865572..29868086-chr22:29877991..29879531,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225465	Chromatin interaction
ENSG00000100285	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12484616	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs174714	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs174723	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs174724	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1974480	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3804076	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7289240	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8136014	0.80[ASN][1000 genomes]
rs9608769	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv1062039	chr22:29854861-29889201	Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv438344	chr22:29856079-29886043	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28380	THOC5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29850600-29867200	Weak transcription	Ovary	ovary
2	chr22:29861600-29873200	Weak transcription	Brain Anterior Caudate	brain
3	chr22:29865600-29866600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr22:29865800-29866600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr22:29865800-29866600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr22:29865800-29866600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr22:29865800-29866800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:29865800-29868600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr22:29866000-29866600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr22:29866000-29866600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr22:29866000-29866600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:29866000-29866600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr22:29866000-29866600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr22:29866000-29866600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr22:29866000-29866600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
16	chr22:29866000-29866600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr22:29866000-29866600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr22:29866000-29866600	Active TSS	A549	lung
19	chr22:29866000-29866600	Active TSS	Hela-S3	cervix
20	chr22:29866000-29866600	Flanking Bivalent TSS/Enh	HepG2	liver
21	chr22:29866000-29866800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr22:29866000-29866800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:29866000-29866800	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr22:29866000-29866800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr22:29866000-29866800	Enhancers	Liver	Liver
26	chr22:29866000-29866800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr22:29866000-29866800	Flanking Active TSS	Placenta	Placenta
28	chr22:29866000-29866800	Enhancers	Lung	lung
29	chr22:29866000-29866800	Flanking Bivalent TSS/Enh	Dnd41	blood
30	chr22:29866000-29866800	Flanking Active TSS	HMEC	breast
31	chr22:29866000-29866800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
32	chr22:29866200-29866600	Active TSS	H1 Cell Line	embryonic stem cell
33	chr22:29866200-29866600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr22:29866200-29866600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr22:29866200-29866600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr22:29866200-29866600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:29866200-29866600	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr22:29866200-29866600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr22:29866200-29866600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
40	chr22:29866200-29866600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr22:29866200-29866600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr22:29866200-29866600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr22:29866200-29866600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr22:29866200-29866600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr22:29866200-29866600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr22:29866200-29866600	Active TSS	Brain Cingulate Gyrus	brain
47	chr22:29866200-29866600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
48	chr22:29866200-29866600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr22:29866200-29866600	Bivalent/Poised TSS	Colonic Mucosa	Colon
50	chr22:29866200-29866600	Flanking Bivalent TSS/Enh	Esophagus	oesophagus

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