Variant report

Variant	rs1919420
Chromosome Location	chr2:51718110-51718111
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1112550	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11563000	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11563001	0.84[ASN][1000 genomes]
rs11563147	0.80[CHB][hapmap];0.88[CHD][hapmap];0.80[ASN][1000 genomes]
rs11563170	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13010068	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13027868	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1406427	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1406428	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1528794	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1534609	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1534610	0.81[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1919425	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1919426	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2049737	0.81[ASN][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	nsv1007188	chr2:51135645-51821787	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535704	chr2:51135645-51821787	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv948449	chr2:51152019-51735494	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1001552	chr2:51225970-52139741	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv535708	chr2:51225970-52139741	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv821624	chr2:51513925-51844864	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1007229	chr2:51689306-51721377	Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1011021	chr2:51712589-51803683	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1919420	NRXN1	cis	parietal	SCAN
rs1919420	FXC1	trans	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:51717800-51718200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:51718000-51718200	Enhancers	Aorta	Aorta

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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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