Variant report

Variant	rs62342528
Chromosome Location	chr5:7884141-7884142
allele	C/G
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	POLR2A	chr5:7883934-7884262	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7868654..7870915-chr5:7883209..7885227,2	MCF-7	breast:

Variant related genes	Relation type
MTRR	TF binding region
ENSG00000124275	Chromatin interaction
ENSG00000124279	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10066017	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10512930	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10520873	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12186809	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16879418	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16879420	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17267793	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776457	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776465	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3797191	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822441	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55872008	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56149723	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57240487	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57989551	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62342552	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62342558	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62345660	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67514505	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67902045	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7703033	0.90[EUR][1000 genomes];0.97[ASN][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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62342528	FASTKD3	Cis_1M	lymphoblastoid	RTeQTL
rs62342528	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
3	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:7871400-7902400	Strong transcription	K562	blood
7	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:7871600-7886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:7871600-7887200	Strong transcription	Fetal Thymus	thymus
10	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
11	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:7871800-7884800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:7872000-7886400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
19	chr5:7872800-7887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:7873200-7903400	Strong transcription	Dnd41	blood
22	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
23	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
25	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:7874200-7887000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
28	chr5:7874800-7887400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:7874800-7887600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:7875400-7884200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr5:7875400-7884600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:7875400-7886200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:7875400-7887200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:7875400-7887400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:7875400-7895200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr5:7875600-7886200	Strong transcription	Ovary	ovary
42	chr5:7875600-7886200	Strong transcription	Thymus	Thymus
43	chr5:7875600-7886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:7875600-7887200	Strong transcription	Fetal Brain Female	brain
45	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
46	chr5:7875800-7884800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr5:7877600-7886200	Strong transcription	Fetal Stomach	stomach
48	chr5:7877800-7884800	Genic enhancers	Brain Inferior Temporal Lobe	brain
49	chr5:7878000-7884200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:7878000-7886000	Genic enhancers	Brain Angular Gyrus	brain

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