Variant report

Variant	rs4616638
Chromosome Location	chr3:143735423-143735424
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143733934..143736908-chr3:143779115..143781560,2	K562	blood:
2	chr3:143735422..143737968-chr3:143770929..143772909,2	K562	blood:
3	chr3:143729064..143730884-chr3:143734825..143736583,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1025984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10513234	0.95[CEU][hapmap]
rs10513235	0.91[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11914731	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13067695	0.90[ASN][1000 genomes]
rs13068298	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs13078840	0.91[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs13081286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13086088	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466941	0.96[CEU][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs16854772	0.84[EUR][1000 genomes]
rs16854816	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16854819	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16854884	0.90[ASN][1000 genomes]
rs16854886	0.90[ASN][1000 genomes]
rs17602500	0.84[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs17667256	0.84[CEU][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1867608	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867609	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1898265	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1961542	0.90[ASN][1000 genomes]
rs1979910	0.91[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs1992093	0.84[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs2011080	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164554	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279856	0.84[CEU][hapmap]
rs2370171	0.90[ASN][1000 genomes]
rs34372603	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34379944	0.91[AMR][1000 genomes]
rs34683397	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35067746	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35085196	0.88[EUR][1000 genomes]
rs35193361	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35309714	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35629416	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35649888	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35788195	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35796781	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35877644	0.84[EUR][1000 genomes]
rs35885310	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35887108	0.90[ASN][1000 genomes]
rs35959290	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4527375	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4561830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611822	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4613453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56196484	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59768870	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60367530	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60676654	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62268458	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62269895	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440210	0.91[CEU][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs6440212	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766544	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766685	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767236	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs6768153	0.95[CEU][hapmap]
rs6769910	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6778627	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6779321	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783089	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6791078	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6796460	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721572	0.80[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs7610378	0.91[CEU][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs7611326	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637912	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639366	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642551	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642774	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646187	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650145	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650172	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920159	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9755502	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9755515	0.86[EUR][1000 genomes];0.95[ASN][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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4616638	CHST2	cis	parietal	SCAN
rs4616638	C3orf58	cis	cerebellum	SCAN
rs4616638	HPS3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143699200-143737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:143731400-143736800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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