Variant report

Variant	rs7647491
Chromosome Location	chr3:59827390-59827391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11130736	0.85[GIH][hapmap]
rs11130739	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12487204	0.80[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1905863	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs2253211	0.90[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3112497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs499323	0.81[CHB][hapmap]
rs610766	0.83[GIH][hapmap]
rs615542	0.83[AFR][1000 genomes]
rs633189	0.90[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs639244	0.85[CHB][hapmap]
rs6446085	0.81[CHB][hapmap]
rs646372	0.81[CHB][hapmap];0.83[GIH][hapmap]
rs652105	0.81[CHB][hapmap]
rs681119	0.81[CHB][hapmap]
rs684584	0.80[CHB][hapmap];0.83[GIH][hapmap]
rs7621132	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[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	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv1003387	chr3:59756364-59831340	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv460563	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv590383	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	nsv876837	chr3:59800539-59842644	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7647491	CADPS	cis	cerebellum	SCAN
rs7647491	PIP5K1B	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59825200-59827400	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr3:59825200-59828000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr3:59825400-59827400	Enhancers	Primary T cells fromperipheralblood	blood
4	chr3:59825400-59827400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr3:59825400-59828200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:59826600-59829600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:59827000-59828400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:59827000-59842800	Weak transcription	Thymus	Thymus
9	chr3:59827200-59831800	Weak transcription	Primary T cells from cord blood	blood
10	chr3:59827200-59843400	Weak transcription	Dnd41	blood

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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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