Variant report

Variant	rs3908502
Chromosome Location	chr1:180591237-180591238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180588663..180591618-chr1:180597337..180599077,2	K562	blood:
2	chr1:180588580..180592293-chr1:180593083..180599077,8	K562	blood:
3	chr1:180552552..180554229-chr1:180589364..180592106,2	MCF-7	breast:
4	chr1:180590595..180593349-chr1:180600520..180602440,3	K562	blood:
5	chr1:180583942..180586396-chr1:180589290..180591332,2	MCF-7	breast:
6	chr1:180579138..180584486-chr1:180589847..180594311,7	K562	blood:
7	chr1:180590033..180591924-chr1:180592968..180595550,2	MCF-7	breast:
8	chr1:180470439..180473404-chr1:180588750..180591613,3	K562	blood:
9	chr1:180590595..180597087-chr1:180599417..180603981,6	K562	blood:
10	chr1:180581736..180587616-chr1:180588288..180595360,13	K562	blood:
11	chr1:180501965..180504289-chr1:180591221..180593705,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10157637	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737349	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331546	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331753	0.93[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs2944259	0.92[MEX][hapmap]
rs3903980	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903981	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651074	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651075	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652524	0.93[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425648	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656378	0.92[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664826	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548318	0.92[MEX][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3908502	PAPPA2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180581800-180600600	Weak transcription	Fetal Heart	heart
2	chr1:180586800-180594400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:180587400-180592800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:180587600-180593200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:180589400-180591400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:180590600-180593400	Enhancers	K562	blood
7	chr1:180591200-180592400	Enhancers	H9 Derived Neuron 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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