Variant report

Variant	rs7568888
Chromosome Location	chr2:50245829-50245830
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]
rs10172768	0.90[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11891637	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11893341	0.80[EUR][1000 genomes]
rs11897683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12469906	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17039606	0.80[EUR][1000 genomes]
rs17039676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17492567	0.90[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17493894	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17494917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730936	0.81[ASW][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs6745029	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7571903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604754	0.90[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.85[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	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv581837	chr2:50230334-50268616	Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1011144	chr2:50231111-50270096	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv915588	chr2:50235306-50268306	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv431002	chr2:50243349-50259749	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7568888	NRXN1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50242600-50246000	Enhancers	Brain Germinal Matrix	brain
2	chr2:50244000-50246200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:50244600-50246600	Enhancers	Hela-S3	cervix
4	chr2:50245000-50246000	Enhancers	Brain Substantia Nigra	brain
5	chr2:50245400-50246000	Enhancers	Brain Hippocampus Middle	brain
6	chr2:50245400-50246000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr2:50245400-50246000	Enhancers	Fetal Brain Female	brain
8	chr2:50245400-50246400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:50245600-50246000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr2:50245600-50246000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:50245600-50246400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr2:50245600-50246400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:50245800-50246200	Enhancers	HUES64 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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