Variant report

Variant	rs1423000
Chromosome Location	chr5:147450806-147450807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:147449509..147451055-chr5:147462616..147464573,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10038561	0.85[EUR][1000 genomes]
rs10038991	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10059850	0.86[EUR][1000 genomes]
rs10060214	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064815	0.81[AFR][1000 genomes]
rs10065129	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10069070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069697	0.86[ASN][1000 genomes]
rs10073775	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1007977	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1007978	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213857	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11168017	0.82[CEU][hapmap]
rs11745768	1.00[YRI][hapmap]
rs12108690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519144	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519499	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12521759	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521761	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422992	0.81[CEU][hapmap]
rs1422993	0.86[ASN][1000 genomes]
rs1422995	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1422996	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423002	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423005	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423006	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423008	0.81[AFR][1000 genomes]
rs1609851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862439	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862445	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862446	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287772	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2895729	0.84[CEU][hapmap]
rs3752676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777140	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777143	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815735	0.88[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3815737	0.87[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3822744	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4333302	0.87[EUR][1000 genomes]
rs4357026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4472254	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4510567	0.85[EUR][1000 genomes]
rs4519912	0.96[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529181	0.92[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4610447	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705223	0.88[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57930479	0.82[ASN][1000 genomes]
rs62388364	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580517	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580518	0.85[EUR][1000 genomes]
rs6580519	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6580520	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6864564	0.87[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs6864920	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6872218	0.84[ASN][1000 genomes]
rs6872326	0.83[ASN][1000 genomes]
rs6876628	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886271	0.86[ASN][1000 genomes]
rs6889688	0.87[EUR][1000 genomes]
rs6891892	0.86[ASN][1000 genomes]
rs6894384	0.85[EUR][1000 genomes]
rs6895078	0.86[ASN][1000 genomes]
rs6896914	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7728739	0.86[ASN][1000 genomes]
rs9325061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325068	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325069	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9325073	0.83[ASN][1000 genomes]
rs9325074	0.83[ASN][1000 genomes]
rs9325075	0.83[ASN][1000 genomes]
rs986493	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986494	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap]
rs986495	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988885	0.88[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][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	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	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
3	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
4	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
5	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1423000	SPINK5	cis	Thyroid	GTEx
rs1423000	ZNF300P1	cis	parietal	SCAN
rs1423000	ANXA6	cis	cerebellum	SCAN
rs1423000	SPINK5	cis	Muscle Skeletal	GTEx
rs1423000	SPINK5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:14 , 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	chr5:147440400-147452800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:147443800-147455400	Weak transcription	Esophagus	oesophagus
5	chr5:147449600-147451000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:147449800-147453000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:147450000-147453000	Enhancers	NHEK	skin
8	chr5:147450200-147451000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:147450400-147452800	Enhancers	HMEC	breast
10	chr5:147450400-147469000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:147450600-147468600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:147450800-147451200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:147450800-147451800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:147450800-147474000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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