Variant report

Variant	rs4603401
Chromosome Location	chr13:29740450-29740451
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10161955	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029190	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12429003	1.00[JPT][hapmap]
rs1335653	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1360857	1.00[JPT][hapmap]
rs1360858	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1541133	1.00[JPT][hapmap]
rs1577478	1.00[JPT][hapmap]
rs17575256	0.87[AMR][1000 genomes]
rs1887747	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1999717	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2050463	1.00[JPT][hapmap]
rs4098154	1.00[JPT][hapmap]
rs4146404	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4146405	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4769005	1.00[JPT][hapmap]
rs4769006	1.00[JPT][hapmap]
rs4769008	1.00[JPT][hapmap]
rs4769688	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4769689	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4769704	1.00[JPT][hapmap]
rs6490365	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs6490368	1.00[JPT][hapmap]
rs6490370	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs6490376	1.00[JPT][hapmap]
rs7322266	1.00[JPT][hapmap]
rs7337839	1.00[JPT][hapmap]
rs7981178	1.00[JPT][hapmap]
rs7981243	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7981637	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7982062	1.00[JPT][hapmap]
rs7982077	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7985145	1.00[JPT][hapmap]
rs7998019	1.00[JPT][hapmap]
rs7999446	1.00[JPT][hapmap]
rs7999907	1.00[JPT][hapmap]
rs8001430	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs9314942	1.00[JPT][hapmap]
rs9314944	1.00[JPT][hapmap]
rs9550453	1.00[JPT][hapmap]
rs9578074	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9579292	0.92[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9579299	0.82[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs9579300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9579308	1.00[JPT][hapmap]

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	nsv533835	chr13:29141132-29962069	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3406145	chr13:29616606-29917459	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899957	chr13:29720732-29820422	Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv455851	chr13:29728058-29746494	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv561391	chr13:29728058-29746494	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv427927	chr13:29729315-30062054	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4603401	MTMR6	cis	cerebellum	SCAN
rs4603401	SHISA2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:29734400-29752600	Weak transcription	Aorta	Aorta
2	chr13:29738600-29743800	Weak transcription	Fetal Stomach	stomach
3	chr13:29739200-29740600	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr13:29739200-29740800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr13:29739400-29740600	Enhancers	GM12878-XiMat	blood
6	chr13:29740200-29742600	Weak transcription	Fetal Heart	heart

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