Variant report

Variant	rs4339838
Chromosome Location	chr1:166082113-166082114
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	chr1:166080632..166082845-chr1:166085034..166087469,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1002160	0.96[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.93[EUR][1000 genomes]
rs10753704	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800183	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs10800184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10800186	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800187	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800192	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800193	0.94[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918344	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918345	0.87[GIH][hapmap];0.83[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs10918347	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918348	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918349	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918362	0.92[EUR][1000 genomes]
rs10918367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918368	1.00[ASW][hapmap];1.00[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];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918369	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10918370	0.93[EUR][1000 genomes]
rs10918371	0.92[YRI][hapmap];0.93[EUR][1000 genomes]
rs10918372	0.92[YRI][hapmap];0.93[EUR][1000 genomes]
rs10918373	0.92[EUR][1000 genomes]
rs10918375	0.92[EUR][1000 genomes]
rs11487531	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11590461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12030010	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12065238	0.93[EUR][1000 genomes]
rs12090916	0.84[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs12097635	0.96[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.93[EUR][1000 genomes]
rs12123839	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12145793	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12756802	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718625	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34402000	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4072242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074897	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4147071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147482	0.87[GIH][hapmap];0.92[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4542195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4657520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4657522	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55704823	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56044172	0.93[EUR][1000 genomes]
rs59317225	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs59384574	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426968	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6426970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659245	0.93[EUR][1000 genomes]
rs6664520	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6692196	0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6698285	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6698973	0.82[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs6700318	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700427	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72703921	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs731264	0.93[EUR][1000 genomes]
rs7513325	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7521995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7530896	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4339838	TBX19	cis	parietal	SCAN
rs4339838	TIPRL	cis	cerebellum	SCAN
rs4339838	RCSD1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166080400-166087000	Weak transcription	Left Ventricle	heart
2	chr1:166080800-166104200	Weak transcription	Pancreas	Pancrea
3	chr1:166081000-166082600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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