Variant report

Variant	rs62482406
Chromosome Location	chr7:102990099-102990100
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr7:102990083-102990272	K562	blood:	n/a	n/a
2	EGR1	chr7:102989965-102990338	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102989850..102992872-chr7:102995534..102998774,5	K562	blood:
2	chr7:102983625..102990524-chr7:102994295..102998538,7	MCF-7	breast:
3	chr7:102986930..102989568-chr7:102989846..102992795,3	K562	blood:

Variant related genes	Relation type
PSMC2	TF binding region
DNAJC2	TF binding region
ENSG00000235354	Chromatin interaction
ENSG00000161057	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10271758	0.96[ASN][1000 genomes]
rs11978339	1.00[ASN][1000 genomes]
rs17136728	1.00[ASN][1000 genomes]
rs17680523	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3087615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35399723	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729911	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482370	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62482394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482397	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482403	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62482404	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62482405	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6972190	0.85[ASN][1000 genomes]
rs73175837	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175852	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62482406	RP11-401L13.5	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102987400-102990400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:102988000-102990600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:102988600-102990800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr7:102988600-103002400	Weak transcription	Spleen	Spleen
5	chr7:102988800-102990200	Flanking Active TSS	Liver	Liver
6	chr7:102988800-102990400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:102989000-102990200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:102989000-102990200	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr7:102989000-102990800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr7:102989000-103006200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:102989200-102990200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:102989200-102990200	Enhancers	Left Ventricle	heart
13	chr7:102989200-102990200	Enhancers	Lung	lung
14	chr7:102989200-102990800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr7:102989200-102990800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:102989200-102991000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:102989200-102991000	Weak transcription	Gastric	stomach
18	chr7:102989200-102991000	Weak transcription	Right Ventricle	heart
19	chr7:102989200-102991200	Enhancers	Primary B cells from peripheral blood	blood
20	chr7:102989200-102991400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr7:102989200-102992200	Enhancers	Colon Smooth Muscle	Colon
22	chr7:102989200-102992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr7:102989200-102993200	Weak transcription	Aorta	Aorta
24	chr7:102989200-102994800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:102989200-102995800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr7:102989200-103002400	Weak transcription	Esophagus	oesophagus
27	chr7:102989200-103006200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:102989200-103007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:102989200-103010600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:102989200-103011400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:102989200-103013200	Weak transcription	Stomach Mucosa	stomach
32	chr7:102989400-102990200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:102989400-102990400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:102989400-102990600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:102989400-102990600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr7:102989400-102990800	Transcr. at gene 5' and 3'	K562	blood
37	chr7:102989400-102991000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr7:102989400-102991200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr7:102989400-102991600	Weak transcription	Placenta	Placenta
40	chr7:102989400-102992400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr7:102989400-102993000	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:102989600-102990200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:102989600-102990200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr7:102989600-102990200	Enhancers	Fetal Brain Male	brain
45	chr7:102989600-102990200	Weak transcription	Fetal Kidney	kidney
46	chr7:102989600-102990200	Enhancers	HSMMtube	muscle
47	chr7:102989600-102990400	Enhancers	Primary hematopoietic stem cells	blood
48	chr7:102989600-102990400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:102989600-102990600	Enhancers	Brain Hippocampus Middle	brain
50	chr7:102989600-102990600	Enhancers	Brain Inferior Temporal Lobe	brain

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