Variant report

Variant	rs6580517
Chromosome Location	chr5:147471137-147471138
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10038561	0.87[EUR][1000 genomes]
rs10038991	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10059850	0.86[EUR][1000 genomes]
rs10060214	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10065129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069070	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10069697	0.90[ASN][1000 genomes]
rs10073775	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1007977	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1007978	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1017222	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10213857	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12108690	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12519144	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12519499	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12521759	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12521761	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1363729	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1422993	0.90[ASN][1000 genomes]
rs1422995	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422996	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423000	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423001	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423002	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423003	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423004	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423005	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423006	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423007	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1609851	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1833768	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1862439	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862445	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862446	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287772	0.83[EUR][1000 genomes]
rs3752676	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756688	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777140	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777143	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3815735	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815737	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822744	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4333302	0.84[EUR][1000 genomes]
rs4354025	0.81[ASN][1000 genomes]
rs4357026	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472254	0.84[EUR][1000 genomes]
rs4510567	0.87[EUR][1000 genomes]
rs4519912	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4529181	0.87[EUR][1000 genomes]
rs4610447	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705223	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57930479	0.86[ASN][1000 genomes]
rs62388364	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580518	0.87[EUR][1000 genomes]
rs6580519	0.85[EUR][1000 genomes]
rs6580520	0.85[EUR][1000 genomes]
rs6864564	0.86[EUR][1000 genomes]
rs6864920	0.85[EUR][1000 genomes]
rs6872218	0.88[ASN][1000 genomes]
rs6872326	0.86[ASN][1000 genomes]
rs6876628	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6886271	0.90[ASN][1000 genomes]
rs6889688	0.84[EUR][1000 genomes]
rs6891892	0.90[ASN][1000 genomes]
rs6894384	0.87[EUR][1000 genomes]
rs6895078	0.90[ASN][1000 genomes]
rs6896914	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7728739	0.90[ASN][1000 genomes]
rs9325061	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325064	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325066	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325068	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325069	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9325073	0.86[ASN][1000 genomes]
rs9325074	0.86[ASN][1000 genomes]
rs9325075	0.86[ASN][1000 genomes]
rs986493	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs986495	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs988885	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6580517	SPINK5	cis	Muscle Skeletal	GTEx
rs6580517	SPINK5	cis	Thyroid	GTEx
rs6580517	SPINK5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147450800-147474000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:147462600-147471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:147464200-147491200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:147464400-147488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:147466200-147471600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:147469200-147471600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:147469200-147471600	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:147469200-147481400	Weak transcription	Esophagus	oesophagus
9	chr5:147469400-147471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:147469800-147472000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:147469800-147472200	Flanking Active TSS	NHEK	skin
12	chr5:147470000-147473000	Weak transcription	Liver	Liver
13	chr5:147470200-147471200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr5:147470200-147481200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:147470400-147518400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:147470600-147471600	Weak transcription	Fetal Lung	lung
17	chr5:147470600-147471600	Weak transcription	Stomach Mucosa	stomach
18	chr5:147470600-147508400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:147470600-147509000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:147470800-147471200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:147470800-147471600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:147470800-147472400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr5:147470800-147472600	Enhancers	HUVEC	blood vessel
24	chr5:147470800-147473400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:147470800-147473600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:147471000-147471200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:147471000-147471200	Flanking Active TSS	Hela-S3	cervix
28	chr5:147471000-147471400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:147471000-147471400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:147471000-147471400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:147471000-147471400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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