Variant report

Variant	rs11711227
Chromosome Location	chr3:60030402-60030403
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:18)

rs_ID	r²[population]
rs11130751	0.85[CEU][hapmap]
rs11718957	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11718994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13062399	0.89[CEU][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13066837	0.86[CHB][hapmap]
rs13081934	0.93[CEU][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13088111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs212045	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs34476175	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35138137	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3845972	0.83[GIH][hapmap];0.83[ASN][1000 genomes]
rs3845973	0.86[MEX][hapmap]
rs3856663	0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs3856664	0.84[AMR][1000 genomes]
rs3856665	0.84[AMR][1000 genomes]
rs62238444	0.86[EUR][1000 genomes]
rs7433134	0.82[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9311746	0.92[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv876839	chr3:60024084-60039488	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11711227	FEZF2	cis	cerebellum	SCAN
rs11711227	SYNPR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60021000-60031600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:60026600-60033600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:60027400-60030600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:60027600-60030800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:60029200-60031000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:60030000-60030600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:60030000-60031000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:60030200-60031200	Strong transcription	Fetal Thymus	thymus
9	chr3:60030400-60031600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:60030400-60031800	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr3:60030400-60032200	ZNF genes & repeats	Dnd41	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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