Variant report

Variant	rs10052211
Chromosome Location	chr5:147454141-147454142
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10213873	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10477360	0.88[ASW][hapmap];0.91[CHD][hapmap];0.88[YRI][hapmap]
rs11168017	0.82[CEU][hapmap]
rs11168019	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168020	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168021	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168022	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168023	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168025	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11948406	0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11948461	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11955201	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11958432	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11959273	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12514503	0.92[CEU][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12657443	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12657460	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13160193	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160662	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13172395	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13181329	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1422991	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17775319	0.93[CEU][hapmap]
rs1978446	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1978447	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1978448	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2052531	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2161434	0.80[CHB][hapmap]
rs2303061	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303062	0.93[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303063	0.89[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303065	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303066	0.93[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303067	0.93[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303068	0.93[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303071	0.93[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34482796	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35803917	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3815736	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4519913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388363	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6580521	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]
rs6580522	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6870820	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6872265	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6892205	0.93[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6896303	0.93[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7445392	0.92[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700488	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7711927	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7711953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712427	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7724165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880687	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9325065	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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	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
rs10052211	SPINK5	cis	Thyroid	GTEx
rs10052211	SPINK5	cis	Muscle Skeletal	GTEx
rs10052211	SPINK5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:9 , 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	chr5:147437800-147463800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:147443800-147455400	Weak transcription	Esophagus	oesophagus
4	chr5:147450400-147469000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:147450600-147468600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:147450800-147474000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:147451000-147470000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:147452800-147454200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:147454000-147470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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