Variant report

Variant	rs3756688
Chromosome Location	chr5:147442779-147442780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10038561	0.82[EUR][1000 genomes]
rs10038991	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10059850	0.83[EUR][1000 genomes]
rs10060214	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064815	0.81[AFR][1000 genomes]
rs10065129	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10069070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069697	0.86[ASN][1000 genomes]
rs10073775	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1007977	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1007978	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213857	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168017	0.82[CEU][hapmap]
rs11745768	1.00[YRI][hapmap]
rs12108690	1.00[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];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519144	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519499	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12521759	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521761	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422992	0.81[CEU][hapmap]
rs1422993	0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs1422995	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1422996	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423001	1.00[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];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423002	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423005	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423006	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423008	0.81[AFR][1000 genomes]
rs1609851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862439	0.88[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862445	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862446	0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287772	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2895729	0.84[CEU][hapmap]
rs3752676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777140	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777143	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815735	0.88[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3815737	0.87[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3822744	0.96[CEU][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]
rs4333302	0.83[EUR][1000 genomes]
rs4357026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4472254	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4510567	0.82[EUR][1000 genomes]
rs4519912	0.96[CEU][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529181	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4610447	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705223	0.88[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57930479	0.82[ASN][1000 genomes]
rs62388364	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580517	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580518	0.82[EUR][1000 genomes]
rs6580519	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs6580520	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs6864564	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs6864920	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs6872218	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs6872326	0.83[ASN][1000 genomes]
rs6876628	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886271	0.86[ASN][1000 genomes]
rs6889688	0.83[EUR][1000 genomes]
rs6891892	0.86[ASN][1000 genomes]
rs6894384	0.82[EUR][1000 genomes]
rs6895078	0.86[ASN][1000 genomes]
rs6896914	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7728739	0.86[ASN][1000 genomes]
rs9325061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325068	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325069	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9325073	0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs9325074	0.83[ASN][1000 genomes]
rs9325075	0.83[ASN][1000 genomes]
rs986493	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986494	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs986495	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988885	0.88[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033838	chr5:147360521-147484014	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv933016	chr5:147395849-147453701	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv933225	chr5:147395849-147486560	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1834529	chr5:147442199-147456843	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3756688	SPINK5	cis	Heart Left Ventricle	GTEx
rs3756688	ANXA6	cis	cerebellum	SCAN
rs3756688	SPINK5	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147437200-147457400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:147437800-147450200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:147437800-147463800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:147440400-147449600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:147440400-147452800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:147441000-147443200	Weak transcription	NHEK	skin
7	chr5:147441000-147443600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:147442200-147443600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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