Variant report

Variant	rs13130041
Chromosome Location	chr4:88229139-88229140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10001545	0.92[ASN][1000 genomes]
rs10006766	0.96[GIH][hapmap]
rs10022237	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10029254	1.00[YRI][hapmap]
rs10032386	1.00[YRI][hapmap]
rs10032710	1.00[YRI][hapmap]
rs10034849	1.00[YRI][hapmap]
rs10084835	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10433879	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10433937	1.00[ASW][hapmap];0.95[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];1.00[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]
rs10440365	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11727374	0.91[ASN][1000 genomes]
rs11735092	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11935592	0.92[ASN][1000 genomes]
rs13118664	0.82[CEU][hapmap];0.94[CHD][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13119654	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13130929	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13137873	0.96[GIH][hapmap]
rs13140105	0.87[ASN][1000 genomes]
rs13142110	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13142655	0.87[ASN][1000 genomes]
rs13150068	0.93[ASN][1000 genomes]
rs13150834	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28418877	0.92[ASN][1000 genomes]
rs28419230	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28439498	0.90[ASN][1000 genomes]
rs28456144	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28528308	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28636836	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28657030	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28664118	0.92[ASN][1000 genomes]
rs28679728	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4089	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4577539	1.00[YRI][hapmap]
rs4998663	0.92[ASN][1000 genomes]
rs6531967	0.87[ASN][1000 genomes]
rs6834488	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6850131	0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6850509	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7663544	0.83[ASN][1000 genomes]
rs7684895	0.92[ASN][1000 genomes]
rs7694379	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9992651	0.82[CEU][hapmap];0.94[CHD][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv879527	chr4:88194170-88250203	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	esv1802846	chr4:88211056-88246450	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13130041	DMP1	cis	parietal	SCAN
rs13130041	HSD17B11	cis	parietal	SCAN
rs13130041	HSD17B13	cis	parietal	SCAN
rs13130041	HSD17B13	cis	cerebellum	SCAN
rs13130041	SLC10A6	cis	cerebellum	SCAN
rs13130041	HSD17B13	cis	Nerve Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88225400-88237800	Strong transcription	Liver	Liver
2	chr4:88226400-88231600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:88228000-88239600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:88228400-88237800	Weak transcription	Hela-S3	cervix
5	chr4:88229000-88229200	Enhancers	A549	lung
6	chr4:88229000-88235600	Weak transcription	Pancreas	Pancrea
7	chr4:88229000-88245000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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