Variant report

Variant	rs223621
Chromosome Location	chr2:32030492-32030493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10439444	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap]
rs1090825	0.88[EUR][1000 genomes]
rs1090828	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12475443	0.81[EUR][1000 genomes]
rs1272585	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs160797	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs160801	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs160803	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs160804	0.82[ASN][1000 genomes]
rs160805	0.82[ASN][1000 genomes]
rs223649	0.88[ASN][1000 genomes]
rs223665	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2366297	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs28797569	0.90[ASN][1000 genomes]
rs481126	0.81[EUR][1000 genomes]
rs564310	0.84[EUR][1000 genomes]
rs806584	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3376782	chr2:31861607-32046180	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1015021	chr2:31972738-32030696	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873777	chr2:32019747-32197123	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs223621	NLRC4	cis	lymphoblastoid	seeQTL
rs223621	RASGRP3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32027600-32030800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:32028800-32030800	Weak transcription	Pancreas	Pancrea
3	chr2:32029200-32030800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:32029400-32030800	Weak transcription	Lung	lung

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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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