Variant report

Variant	rs6580521
Chromosome Location	chr5:147474799-147474800
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10041981	0.88[ASN][1000 genomes]
rs10052211	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10213873	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10515602	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10515603	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10875630	0.88[ASN][1000 genomes]
rs11168017	0.85[CEU][hapmap]
rs11168019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168020	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168021	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168023	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168025	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168026	0.91[ASN][1000 genomes]
rs11168027	0.91[ASN][1000 genomes]
rs11168028	0.90[ASN][1000 genomes]
rs11168029	0.88[ASN][1000 genomes]
rs11168030	0.88[ASN][1000 genomes]
rs11168031	0.88[ASN][1000 genomes]
rs11168032	0.88[ASN][1000 genomes]
rs11168033	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1155636	0.88[ASN][1000 genomes]
rs1155637	0.88[ASN][1000 genomes]
rs11741387	0.90[ASN][1000 genomes]
rs11741417	0.90[ASN][1000 genomes]
rs11743440	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11745592	0.91[ASN][1000 genomes]
rs11948406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948461	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11958432	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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187820	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12188819	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12514503	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12518996	0.90[ASN][1000 genomes]
rs12519519	0.91[ASN][1000 genomes]
rs12654179	0.88[ASN][1000 genomes]
rs12657443	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12657460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13160193	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13160662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13172395	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13181329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363722	0.91[ASN][1000 genomes]
rs1363723	0.91[ASN][1000 genomes]
rs1422987	0.83[CHB][hapmap]
rs1422991	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1422994	0.90[ASN][1000 genomes]
rs17704908	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17775319	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1978446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1978447	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1978448	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052531	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2052532	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2052534	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2052535	0.88[ASN][1000 genomes]
rs2052536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2112765	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2112766	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2112767	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2161434	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2303061	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303062	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303063	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303064	0.83[CHB][hapmap]
rs2303065	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303066	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303067	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303068	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303071	0.96[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];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303072	0.88[ASN][1000 genomes]
rs2303073	0.88[ASN][1000 genomes]
rs2400477	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2400478	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2400479	0.91[ASN][1000 genomes]
rs28627452	0.88[ASN][1000 genomes]
rs3088193	0.87[ASN][1000 genomes]
rs33920397	0.91[ASN][1000 genomes]
rs34427102	0.87[ASN][1000 genomes]
rs34482796	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34673384	0.83[ASN][1000 genomes]
rs35803917	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756689	0.88[ASN][1000 genomes]
rs3756690	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3764926	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3764927	0.91[ASN][1000 genomes]
rs3764928	0.91[ASN][1000 genomes]
rs3764930	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3777129	0.83[ASN][1000 genomes]
rs3777134	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3777135	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3777136	0.89[ASN][1000 genomes]
rs3777137	0.89[ASN][1000 genomes]
rs3815736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822745	0.90[ASN][1000 genomes]
rs4235737	0.81[ASN][1000 genomes]
rs4235738	0.81[ASN][1000 genomes]
rs4315912	0.82[ASN][1000 genomes]
rs4334874	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4349706	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4354024	0.82[ASN][1000 genomes]
rs4362935	0.85[ASN][1000 genomes]
rs4368717	0.82[ASN][1000 genomes]
rs4371740	0.82[ASN][1000 genomes]
rs4385198	0.81[ASN][1000 genomes]
rs4440347	0.85[ASN][1000 genomes]
rs4502810	0.86[ASN][1000 genomes]
rs4519913	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4588586	0.83[ASN][1000 genomes]
rs4642357	0.82[ASN][1000 genomes]
rs4705054	0.84[CHB][hapmap]
rs62388363	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580522	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6580524	0.90[ASN][1000 genomes]
rs6868182	0.86[ASN][1000 genomes]
rs6870820	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872265	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6873836	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6875266	0.91[ASN][1000 genomes]
rs6877585	0.87[ASN][1000 genomes]
rs6883868	0.91[ASN][1000 genomes]
rs6892205	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894572	0.91[ASN][1000 genomes]
rs6895434	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6896303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7445392	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7700488	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711927	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711953	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7712427	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7724165	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7725816	0.83[CHB][hapmap]
rs880687	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325065	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580521	SPINK5	cis	Thyroid	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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