Variant report

Variant	rs12541538
Chromosome Location	chr8:4805794-4805795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:4805755..4808307-chr8:4809361..4811905,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10448108	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11783540	0.81[ASW][hapmap];0.82[CEU][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]
rs11783663	0.81[ASW][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap]
rs11986686	0.91[YRI][hapmap]
rs11996410	0.81[ASW][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap]
rs11997499	0.84[YRI][hapmap]
rs11997657	0.91[YRI][hapmap]
rs11998098	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11998341	0.81[ASW][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap]
rs11998370	0.91[YRI][hapmap]
rs12056859	0.80[ASW][hapmap];0.90[YRI][hapmap]
rs12681508	0.95[YRI][hapmap]
rs4360312	0.82[CEU][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]
rs4427198	0.81[ASW][hapmap];0.82[CEU][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]
rs4584160	0.81[ASW][hapmap];0.82[CEU][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]
rs4620305	0.81[ASW][hapmap];0.82[CEU][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap]
rs4875416	0.91[YRI][hapmap]
rs4875418	0.82[ASW][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap]
rs6558949	0.82[JPT][hapmap]
rs6981024	0.86[CHB][hapmap]
rs6986049	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6987219	0.84[ASN][1000 genomes]
rs6988034	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs7003760	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004552	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7004731	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7005814	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7013186	0.85[CEU][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap]
rs7832847	0.85[CEU][hapmap];0.90[YRI][hapmap]

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	nsv609876	chr8:4494811-5092970	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1029480	chr8:4497596-5081032	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv498130	chr8:4532988-5176376	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv889976	chr8:4750266-4824335	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1028542	chr8:4758159-4824005	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1031026	chr8:4771072-5054326	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv889977	chr8:4802438-4820177	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12541538	DEFA6	cis	cerebellum	SCAN
rs12541538	CSMD1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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