Variant report

Variant	rs9999653
Chromosome Location	chr4:56498249-56498250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10000850	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10011137	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11133404	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11935806	0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12498734	0.90[AFR][1000 genomes]
rs12499623	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1488937	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3792703	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs56156718	0.86[ASN][1000 genomes]
rs56268402	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62308711	0.91[ASN][1000 genomes]
rs62308712	0.91[ASN][1000 genomes]
rs62308713	0.91[ASN][1000 genomes]
rs6823777	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6827359	0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879021	chr4:56482750-56648713	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3393088	chr4:56484073-56503988	Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3395811	chr4:56486113-56514675	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9999653	SPINK2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56485400-56498400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:56492600-56498400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:56493400-56500200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:56494000-56500600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:56495800-56499000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:56496200-56498800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:56498000-56498600	Transcr. at gene 5' and 3'	K562	blood
8	chr4:56498000-56499000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr4:56498000-56500200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr4:56498200-56498600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:56498200-56498800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:56498200-56499000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:56498200-56499200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:56498200-56499800	Enhancers	HUES48 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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