Variant report

Variant	rs4679924
Chromosome Location	chr3:160661862-160661863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160659734..160663014-chr3:160666194..160669867,3	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1037888	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10513559	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513562	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs11708076	0.85[ASN][1000 genomes]
rs11708813	0.96[CEU][hapmap]
rs11716265	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11922752	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs12639128	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs13064176	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071909	0.82[EUR][1000 genomes]
rs13073571	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086250	0.96[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs13089559	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092102	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs13097130	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098884	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1374793	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1447618	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1447619	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1447620	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1610158	0.85[CEU][hapmap];0.85[MEX][hapmap]
rs17236725	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs17236746	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17826438	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839021	0.84[EUR][1000 genomes]
rs2121718	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2306061	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs2593812	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs34168351	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34297047	0.85[EUR][1000 genomes]
rs4557202	0.81[CEU][hapmap]
rs4679662	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs4679666	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4679671	0.82[EUR][1000 genomes]
rs4679922	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679926	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5004752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs55672403	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55888276	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61105146	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270274	0.81[EUR][1000 genomes]
rs62270275	0.81[EUR][1000 genomes]
rs62280303	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280331	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62280333	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441339	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6441354	0.80[CEU][hapmap]
rs6764019	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6796201	0.85[EUR][1000 genomes]
rs6799160	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6804650	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806054	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6809177	0.96[CEU][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs723757	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622047	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7628880	0.81[EUR][1000 genomes]
rs7632423	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs778642	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs778643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs778645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs778646	0.86[EUR][1000 genomes]
rs778649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs778653	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs778654	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs778657	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs778663	0.83[EUR][1000 genomes]
rs796609	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs898680	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs898681	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs9290065	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs9790132	0.87[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs980975	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs980976	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9811594	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs9820825	0.82[CEU][hapmap]
rs9831488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9847866	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9860360	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9875200	0.96[CEU][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4679924	NMD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160658800-160667400	Weak transcription	Thymus	Thymus
2	chr3:160659800-160663000	Weak transcription	Liver	Liver
3	chr3:160659800-160666000	Weak transcription	Fetal Kidney	kidney
4	chr3:160660200-160663200	Weak transcription	Colon Smooth Muscle	Colon

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