Variant report

Variant	rs4254189
Chromosome Location	chr13:40212417-40212418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10162010	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10467367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10467368	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4129745	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4132636	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4132637	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4261404	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4275735	0.90[ASN][1000 genomes]
rs4277227	0.86[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4294679	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4300508	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4321067	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4334152	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4363738	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4368051	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4432137	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4457870	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4485233	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4492929	0.91[ASN][1000 genomes]
rs4514547	0.86[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4551909	0.89[ASN][1000 genomes]
rs4556673	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4566029	0.86[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4569133	0.86[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4586300	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4598779	0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4606581	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4636783	0.86[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4941940	0.91[ASN][1000 genomes]
rs4943688	0.91[ASN][1000 genomes]
rs4943689	0.91[ASN][1000 genomes]
rs4943692	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4943693	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6563737	0.91[ASN][1000 genomes]
rs6563738	0.90[ASN][1000 genomes]
rs6563739	0.86[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs6563740	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7320424	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7324826	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7325354	0.92[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs7326555	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7326699	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7327674	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7330016	0.86[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7330515	0.91[ASN][1000 genomes]
rs74044148	0.85[ASN][1000 genomes]
rs7991151	0.86[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7991758	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7993726	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7993729	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7994665	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7998582	0.90[ASN][1000 genomes]
rs7999758	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs9315723	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9315724	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9532416	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9532417	0.91[ASN][1000 genomes]
rs9548872	0.89[ASN][1000 genomes]
rs9548873	0.89[ASN][1000 genomes]
rs9548876	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9548877	0.91[ASN][1000 genomes]
rs9548878	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9548881	0.87[ASN][1000 genomes]
rs9548883	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548884	0.93[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs9548885	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548895	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9566469	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9594362	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9603589	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603591	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9603592	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9603593	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603594	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603597	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9603602	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
5	esv3363652	chr13:40199001-40221148	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv974009	chr13:40212255-40222785	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4254189	C13orf36	cis	parietal	SCAN
rs4254189	COG6	cis	Muscle Skeletal	GTEx
rs4254189	COG6	cis	Adipose Subcutaneous	GTEx
rs4254189	COG6	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40209200-40212800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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