Variant report

Variant	rs563768
Chromosome Location	chr1:77141039-77141040
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1173686	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs1184626	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs484299	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs550021	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs604078	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs621590	0.80[ASN][1000 genomes]
rs628482	0.82[ASN][1000 genomes]
rs636038	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs650427	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs676269	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs677158	0.94[ASN][1000 genomes]
rs680970	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs683148	0.80[ASN][1000 genomes]
rs689423	0.93[EUR][1000 genomes];0.94[ASN][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	nsv997827	chr1:76929028-77201457	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv526433	chr1:77030764-77268215	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1001253	chr1:77077660-77234093	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv870909	chr1:77104773-77195164	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1005649	chr1:77141039-77398747	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs563768	ASB17	cis	cerebellum	SCAN
rs563768	PIGK	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77138800-77141200	Enhancers	Fetal Intestine Small	intestine
2	chr1:77138800-77141400	Enhancers	Fetal Intestine Large	intestine
3	chr1:77139800-77141200	Enhancers	Liver	Liver
4	chr1:77140800-77145400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:77140800-77146000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:77141000-77141400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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