Variant report

Variant	rs4504390
Chromosome Location	chr5:42548024-42548025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10941578	0.91[CEU][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10941579	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11739444	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11740415	0.87[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs11948453	1.00[JPT][hapmap]
rs11949751	0.87[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11955075	0.87[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12516901	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12520276	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12521020	0.87[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13160458	0.92[CEU][hapmap]
rs13176410	0.88[EUR][1000 genomes]
rs28943881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34374598	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34466913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34535288	0.90[EUR][1000 genomes]
rs34895721	0.83[EUR][1000 genomes]
rs35090794	0.94[EUR][1000 genomes]
rs4075783	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4242115	1.00[JPT][hapmap]
rs4305645	1.00[JPT][hapmap]
rs4314405	0.90[JPT][hapmap]
rs4365846	0.94[ASW][hapmap];0.92[CEU][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4368736	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4395642	0.94[ASW][hapmap];0.92[CEU][hapmap];0.83[TSI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4484445	1.00[JPT][hapmap]
rs4489074	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4493680	0.91[CEU][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs4496716	0.91[CEU][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4533898	0.88[ASN][1000 genomes]
rs4554233	1.00[JPT][hapmap]
rs4866791	1.00[JPT][hapmap]
rs4866936	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs55696942	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61197005	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451626	1.00[JPT][hapmap]
rs6859653	0.89[ASW][hapmap];0.88[CEU][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap]
rs6863381	0.80[CEU][hapmap]
rs6865492	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6881929	0.87[CEU][hapmap];0.92[TSI][hapmap]
rs6887718	1.00[JPT][hapmap]
rs6896667	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7703713	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap]
rs7707913	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs7712701	0.91[EUR][1000 genomes]
rs7714392	0.92[EUR][1000 genomes]
rs7721816	1.00[JPT][hapmap]
rs7735889	0.87[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7736209	0.87[CEU][hapmap];0.83[TSI][hapmap];0.89[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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised 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	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4504390	SEPP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42539800-42552000	Weak transcription	Ovary	ovary
2	chr5:42541000-42552400	Weak transcription	Aorta	Aorta
3	chr5:42544200-42551000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:42544400-42549200	Weak transcription	Psoas Muscle	Psoas
5	chr5:42544400-42551000	Weak transcription	Fetal Heart	heart
6	chr5:42544800-42553200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:42545600-42549600	Enhancers	Fetal Lung	lung
8	chr5:42545800-42548400	Enhancers	Liver	Liver
9	chr5:42546400-42548200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:42546400-42548400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr5:42546400-42550400	Enhancers	Fetal Stomach	stomach
12	chr5:42546400-42553800	Enhancers	Adipose Nuclei	Adipose
13	chr5:42546600-42550000	Weak transcription	Right Ventricle	heart
14	chr5:42546600-42550200	Enhancers	Colon Smooth Muscle	Colon
15	chr5:42546600-42552000	Weak transcription	Right Atrium	heart
16	chr5:42546800-42548400	Enhancers	HUVEC	blood vessel
17	chr5:42546800-42548800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:42546800-42549800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:42547000-42548200	Enhancers	NHDF-Ad	bronchial
20	chr5:42547000-42549600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:42547400-42548400	Enhancers	Left Ventricle	heart
22	chr5:42547400-42549400	Enhancers	Rectal Smooth Muscle	rectum
23	chr5:42548000-42548200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:42548000-42549400	Enhancers	Stomach Smooth Muscle	stomach

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