Variant report

Variant	rs4820002
Chromosome Location	chr22:30704065-30704066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30692354..30698688-chr22:30699927..30704803,9	K562	blood:

Variant related genes	Relation type
ENSG00000248751	Chromatin interaction
ENSG00000099992	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13056562	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058084	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058535	1.00[ASN][1000 genomes]
rs17730748	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738020	1.00[ASN][1000 genomes]
rs34102711	1.00[ASN][1000 genomes]
rs34318316	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911581	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34964064	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35074129	1.00[ASN][1000 genomes]
rs35246430	1.00[ASN][1000 genomes]
rs35617977	1.00[ASN][1000 genomes]
rs35960997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449240	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4820834	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820840	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823086	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823087	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67401267	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168654	1.00[ASN][1000 genomes]
rs8139982	0.86[AFR][1000 genomes]
rs8140284	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv984527	chr22:30698358-30732712	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4820002	RP1-130H16.16	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
2	chr22:30686800-30707200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr22:30687400-30706800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr22:30691000-30706800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr22:30695400-30706800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:30697400-30712200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:30698600-30705800	Enhancers	Colon Smooth Muscle	Colon
8	chr22:30698800-30705600	Weak transcription	Ovary	ovary
9	chr22:30698800-30707000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr22:30699200-30704200	Weak transcription	Aorta	Aorta
11	chr22:30699200-30706200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr22:30699600-30706200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:30699600-30715600	Weak transcription	Fetal Brain Female	brain
14	chr22:30699800-30705600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr22:30699800-30710000	Weak transcription	HepG2	liver
16	chr22:30699800-30711600	Enhancers	Stomach Mucosa	stomach
17	chr22:30700000-30710000	Enhancers	HMEC	breast
18	chr22:30700200-30712000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr22:30700200-30712600	Enhancers	Primary hematopoietic stem cells	blood
20	chr22:30700400-30706200	Weak transcription	Brain Germinal Matrix	brain
21	chr22:30700400-30710000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr22:30700400-30714400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr22:30700600-30711200	Enhancers	Placenta	Placenta
24	chr22:30701000-30705400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr22:30701000-30706800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr22:30701200-30704800	Enhancers	K562	blood
27	chr22:30701400-30705600	Weak transcription	Fetal Heart	heart
28	chr22:30701400-30709200	Enhancers	Fetal Kidney	kidney
29	chr22:30701600-30704800	Weak transcription	Small Intestine	intestine
30	chr22:30701800-30706000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr22:30702000-30704200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr22:30702000-30706200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr22:30702000-30706600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr22:30702000-30706600	Enhancers	Colonic Mucosa	Colon
35	chr22:30702000-30707400	Enhancers	NHEK	skin
36	chr22:30702200-30704600	Weak transcription	NH-A	brain
37	chr22:30702200-30705000	Enhancers	Stomach Smooth Muscle	stomach
38	chr22:30702200-30705800	Weak transcription	Brain Angular Gyrus	brain
39	chr22:30702200-30706000	Weak transcription	HSMMtube	muscle
40	chr22:30702200-30706400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr22:30702200-30706400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr22:30702200-30707000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr22:30702400-30704200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:30702400-30704200	Weak transcription	Gastric	stomach
45	chr22:30702400-30704200	Weak transcription	NHDF-Ad	bronchial
46	chr22:30702400-30704200	Weak transcription	NHLF	lung
47	chr22:30702400-30704600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr22:30702400-30706000	Enhancers	Rectal Smooth Muscle	rectum
49	chr22:30702400-30706200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:30702400-30706200	Enhancers	Duodenum Mucosa	Duodenum

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