Variant report

Variant	rs17623890
Chromosome Location	chr5:29151261-29151262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10520947	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1117224	1.00[YRI][hapmap]
rs1603431	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2169887	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34087984	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34759489	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35379691	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71621760	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs980403	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023990	chr5:28917253-29220447	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3528360	chr5:29069255-29548659	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv3528361	chr5:29069255-29548659	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1022253	chr5:29076460-29195987	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1016603	chr5:29102713-29843965	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv537712	chr5:29102713-29843965	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv1030526	chr5:29125802-29204186	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv964827	chr5:29138557-29198352	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17623890	CDH6	cis	parietal	SCAN
rs17623890	MTMR12	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:29148000-29151400	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr5:29148600-29151400	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr5:29149000-29151600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr5:29149200-29153400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:29149400-29151400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr5:29150000-29151400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr5:29150200-29151400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr5:29150200-29151400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:29150800-29151400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr5:29150800-29151400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:29150800-29151400	Enhancers	Colon Smooth Muscle	Colon
12	chr5:29151000-29153200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:29151200-29151400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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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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