Variant report

Variant	rs17663598
Chromosome Location	chr1:212377879-212377880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12022111	0.80[EUR][1000 genomes]
rs12136808	0.82[EUR][1000 genomes]
rs12143853	0.81[CEU][hapmap]
rs1493602	0.83[EUR][1000 genomes]
rs2358446	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs399429	0.82[EUR][1000 genomes]
rs4951580	0.82[EUR][1000 genomes]
rs9793334	0.83[EUR][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17663598	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212368800-212391000	Weak transcription	Thymus	Thymus
2	chr1:212375200-212379600	Enhancers	Placenta	Placenta
3	chr1:212376000-212382400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:212376200-212378000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:212376200-212380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:212376200-212380600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:212376400-212380600	Weak transcription	Left Ventricle	heart
8	chr1:212376600-212378400	Enhancers	Brain Anterior Caudate	brain
9	chr1:212376800-212379000	Weak transcription	K562	blood
10	chr1:212376800-212382400	Weak transcription	HepG2	liver
11	chr1:212377200-212378400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:212377600-212379800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:212377800-212378000	Enhancers	Brain Substantia Nigra	brain
14	chr1:212377800-212378400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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