Variant report

Variant	rs10463396
Chromosome Location	chr5:147415342-147415343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10052211	0.87[ASW][hapmap];0.88[YRI][hapmap]
rs10058108	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062911	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064815	0.81[EUR][1000 genomes]
rs10067434	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463395	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10477360	0.88[ASW][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1363727	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363728	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422982	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422997	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422998	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423008	0.80[EUR][1000 genomes]
rs1549237	0.89[AFR][1000 genomes]
rs17626088	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052529	0.80[EUR][1000 genomes]
rs2216655	0.81[EUR][1000 genomes]
rs2287772	0.84[CEU][hapmap]
rs28576989	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895729	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4415068	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4472254	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap]
rs4529181	0.84[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap]
rs4705218	0.81[EUR][1000 genomes]
rs6580519	0.81[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs6580520	0.81[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs6864564	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap]
rs6864920	0.81[CEU][hapmap]
rs6891643	0.83[EUR][1000 genomes]
rs7701882	0.82[EUR][1000 genomes]
rs7704424	0.83[EUR][1000 genomes]
rs7713918	0.83[EUR][1000 genomes]
rs7716414	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727177	0.93[AFR][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	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10463396	SPINK5	cis	Adipose Subcutaneous	GTEx
rs10463396	SPINK5	cis	Heart Left Ventricle	GTEx
rs10463396	ZNF300P1	cis	parietal	SCAN
rs10463396	SPINK5	cis	Muscle Skeletal	GTEx
rs10463396	SPINK5	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147412800-147418000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:147413600-147434200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:147414400-147415400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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