Variant report

Variant	rs13017988
Chromosome Location	chr2:172759467-172759468
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172749780..172752389-chr2:172759130..172760701,2	K562	blood:
2	chr2:172758196..172760986-chr2:172762704..172765677,2	K562	blood:
3	chr2:172758196..172762608-chr2:172762704..172765555,5	K562	blood:

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10166352	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10177679	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10185633	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10188587	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10196521	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1022358	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10432474	0.81[AFR][1000 genomes]
rs10439296	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10930496	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10930498	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10930500	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1105264	0.83[AFR][1000 genomes]
rs11676484	0.88[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11677573	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[AFR][1000 genomes]
rs11692418	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11695887	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11883977	0.91[ASN][1000 genomes]
rs11887208	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12468218	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12473516	0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs12478215	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12479374	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12617265	1.00[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12619137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692977	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13018515	0.88[AMR][1000 genomes]
rs13021571	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13399316	1.00[ASW][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs1400816	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1443700	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543168	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1607253	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1878583	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1982288	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1996425	0.83[AFR][1000 genomes]
rs2028670	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2028671	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2028672	1.00[JPT][hapmap]
rs2056202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2138873	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2176466	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2292813	0.88[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2292814	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2357064	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2357206	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2357208	1.00[JPT][hapmap]
rs28372952	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[AFR][1000 genomes]
rs2884123	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs312917	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3770443	1.00[JPT][hapmap]
rs3770444	0.82[AFR][1000 genomes]
rs3770453	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs3770457	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3821092	1.00[JPT][hapmap]
rs3821094	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs3821095	0.83[YRI][hapmap]
rs3821096	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs4072279	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4324292	0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668413	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4668415	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668416	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668417	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4668419	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59853867	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6433313	0.94[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs6433315	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs6433317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433318	1.00[ASW][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6433322	0.83[ASW][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs6707142	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6708365	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709299	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6711813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6714214	1.00[ASW][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6726991	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6727459	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6736159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6740705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753859	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6757680	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6758494	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6760680	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7340516	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7371503	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7579509	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7580132	1.00[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7580232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7583860	0.87[AFR][1000 genomes]
rs7588025	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7594478	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs925881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9287948	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs949548	0.94[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs9636293	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs970948	0.94[ASW][hapmap];0.89[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536037	chr2:172745597-172780616	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13017988	AC068039.4	cis	Stomach	GTEx
rs13017988	RAPGEF4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172754400-172759600	Weak transcription	Osteobl	bone
2	chr2:172759400-172759600	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr2:172759400-172759800	Flanking Active TSS	GM12878-XiMat	blood

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