Variant report

Variant	rs6580520
Chromosome Location	chr5:147474671-147474672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10038561	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10038991	0.81[EUR][1000 genomes]
rs10059850	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10060214	0.81[EUR][1000 genomes]
rs10065129	0.84[EUR][1000 genomes]
rs10069070	0.96[CEU][hapmap]
rs10073775	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1007977	0.81[EUR][1000 genomes]
rs1007978	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1017222	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs12108690	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12519144	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12521761	0.81[EUR][1000 genomes]
rs13185274	0.85[JPT][hapmap]
rs1363729	0.96[CEU][hapmap]
rs1422992	0.84[CEU][hapmap]
rs1422995	0.83[EUR][1000 genomes]
rs1422996	0.85[EUR][1000 genomes]
rs1423000	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1423001	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1423002	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1423003	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1423004	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1423005	0.81[EUR][1000 genomes]
rs1423006	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1423007	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs1609851	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1833768	0.81[EUR][1000 genomes]
rs1862439	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs1862445	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1862446	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2287772	0.96[CEU][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2895729	0.81[CEU][hapmap]
rs3752676	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs3756688	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs3777140	0.85[CEU][hapmap]
rs3777143	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs3815735	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs3815737	0.84[CEU][hapmap]
rs3822744	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4333302	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4357026	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs4472254	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4510567	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4519912	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4529181	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4610447	0.83[EUR][1000 genomes]
rs4705223	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs62388364	0.87[EUR][1000 genomes]
rs6580517	0.85[EUR][1000 genomes]
rs6580518	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864564	0.91[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6864920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876628	0.83[EUR][1000 genomes]
rs6889688	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6894384	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896914	0.81[EUR][1000 genomes]
rs7707841	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9325061	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9325064	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9325066	0.81[EUR][1000 genomes]
rs9325068	0.80[EUR][1000 genomes]
rs9325069	0.83[EUR][1000 genomes]
rs986493	0.81[EUR][1000 genomes]
rs986495	0.81[EUR][1000 genomes]
rs988885	0.85[CEU][hapmap];0.83[TSI][hapmap];0.81[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	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	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
3	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
4	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6580520	SPINK5	cis	Thyroid	GTEx
rs6580520	SPINK5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147464200-147491200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:147464400-147488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:147469200-147481400	Weak transcription	Esophagus	oesophagus
4	chr5:147470200-147481200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:147470400-147518400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:147470600-147508400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:147470600-147509000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:147471600-147474800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:147471600-147475000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:147471600-147514800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:147472000-147505000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:147472200-147474800	Enhancers	NHEK	skin
13	chr5:147472400-147479400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:147472600-147475400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:147472600-147497200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:147473400-147475600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:147474000-147475200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:147474200-147475600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:147474200-147479000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:147474200-147513400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:147474600-147474800	Strong transcription	Hela-S3	cervix

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