Variant report

Variant	rs6851997
Chromosome Location	chr4:74679286-74679287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10005565	0.92[EUR][1000 genomes]
rs10009462	0.91[EUR][1000 genomes]
rs10009488	0.92[EUR][1000 genomes]
rs10010970	0.92[EUR][1000 genomes]
rs10012962	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10015626	0.92[EUR][1000 genomes]
rs10019318	0.91[EUR][1000 genomes]
rs10031141	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs10938092	0.86[EUR][1000 genomes]
rs10938094	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10938095	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10938096	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10938097	0.90[EUR][1000 genomes]
rs10938100	0.91[EUR][1000 genomes]
rs10938101	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126647	0.85[EUR][1000 genomes]
rs11730284	0.82[EUR][1000 genomes]
rs11730560	0.86[EUR][1000 genomes]
rs11730667	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs11733222	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11938389	0.91[EUR][1000 genomes]
rs12503139	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12644561	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13112910	0.83[EUR][1000 genomes]
rs13117876	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs13138675	0.80[EUR][1000 genomes]
rs13151869	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16849945	0.86[EUR][1000 genomes]
rs16849958	0.84[EUR][1000 genomes]
rs16850073	0.80[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap]
rs1951235	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1951236	0.84[EUR][1000 genomes]
rs1957070	0.91[EUR][1000 genomes]
rs1957661	0.86[EUR][1000 genomes]
rs2145617	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[TSI][hapmap]
rs2224434	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[TSI][hapmap]
rs2227306	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2227543	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2367276	0.90[EUR][1000 genomes]
rs28609798	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28612337	0.86[EUR][1000 genomes]
rs28833215	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2886920	0.92[EUR][1000 genomes]
rs2886922	0.91[EUR][1000 genomes]
rs4279174	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4549349	0.91[EUR][1000 genomes]
rs4694178	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4694636	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs4694637	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs62312370	0.86[EUR][1000 genomes]
rs6446959	0.86[EUR][1000 genomes]
rs6446960	0.91[EUR][1000 genomes]
rs6446961	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6820848	0.87[EUR][1000 genomes]
rs6831029	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6853679	0.91[EUR][1000 genomes]
rs724398	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7689435	0.91[EUR][1000 genomes]
rs9999262	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999446	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1005231	chr4:74555497-74680079	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6851997	THAP6	cis	parietal	SCAN
rs6851997	ALB	cis	cerebellum	SCAN
rs6851997	SEPT11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74676200-74682200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:74678800-74682200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr4:74679000-74682800	Enhancers	Thymus	Thymus
4	chr4:74679200-74679600	Weak transcription	Dnd41	blood

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