Variant report

Variant	rs4650704
Chromosome Location	chr1:175118923-175118924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10489328	0.91[CEU][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap]
rs12135071	0.98[ASN][1000 genomes]
rs2018318	0.91[CEU][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap]
rs2187958	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs3737933	1.00[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4651335	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56237830	0.98[ASN][1000 genomes]
rs73032636	0.81[AFR][1000 genomes];0.98[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	nsv508648	chr1:175056387-175121913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4650704	CACYBP	cis	cerebellum	SCAN
rs4650704	MRPS14	cis	parietal	SCAN
rs4650704	CACYBP	cis	parietal	SCAN
rs4650704	KIAA0040	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175108000-175119800	Weak transcription	Adipose Nuclei	Adipose
2	chr1:175110200-175127400	Weak transcription	Left Ventricle	heart
3	chr1:175111400-175122600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:175111600-175119600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:175115000-175125000	Weak transcription	Right Atrium	heart
6	chr1:175115800-175120000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:175116000-175119200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:175116200-175119000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:175116200-175120000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:175116400-175119000	Weak transcription	Liver	Liver
11	chr1:175116400-175119200	Weak transcription	Fetal Heart	heart
12	chr1:175116400-175119400	Weak transcription	HMEC	breast
13	chr1:175116400-175121200	Weak transcription	Placenta	Placenta
14	chr1:175116600-175121400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:175116800-175121000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:175117600-175119200	Weak transcription	Fetal Brain Male	brain

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

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