Variant report

Variant	rs11717618
Chromosome Location	chr3:157911656-157911657
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10936131	0.88[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10936132	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1095636	0.89[ASN][1000 genomes]
rs11712563	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715599	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717923	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11719153	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1193511	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1193536	0.85[ASN][1000 genomes]
rs1204957	0.87[ASN][1000 genomes]
rs12053861	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12053865	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12053869	0.92[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12485440	0.86[JPT][hapmap]
rs12634807	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12636733	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12639261	0.87[EUR][1000 genomes]
rs12639310	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12696067	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs13059066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13061378	0.81[JPT][hapmap]
rs1581408	0.82[JPT][hapmap]
rs1608100	0.80[JPT][hapmap]
rs1609525	0.86[JPT][hapmap];0.89[YRI][hapmap]
rs1724666	0.96[ASN][1000 genomes]
rs1724679	0.89[ASN][1000 genomes]
rs1729998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1730029	0.99[ASN][1000 genomes]
rs1730032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1730044	0.93[ASN][1000 genomes]
rs1730099	0.92[CHB][hapmap];0.82[JPT][hapmap];0.99[ASN][1000 genomes]
rs17683939	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1851062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1915935	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1918000	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2139696	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2682402	0.87[ASN][1000 genomes]
rs2682407	0.96[ASN][1000 genomes]
rs2693540	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2693546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34434866	0.87[EUR][1000 genomes]
rs4346508	0.85[JPT][hapmap]
rs4431056	0.82[JPT][hapmap]
rs4680412	0.86[JPT][hapmap]
rs4680413	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4680421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680425	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4680428	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4680432	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs56123505	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs57665991	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58195752	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs58925169	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs60962704	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441193	0.92[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6762706	0.99[ASN][1000 genomes]
rs6767494	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6772246	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6784968	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6790608	0.82[JPT][hapmap]
rs6800218	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6800853	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6803630	0.80[JPT][hapmap]
rs6807468	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs696715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs698975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs698976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs698977	0.96[ASN][1000 genomes]
rs698979	0.96[ASN][1000 genomes]
rs698981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs698982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs698983	0.94[ASN][1000 genomes]
rs698984	0.96[ASN][1000 genomes]
rs698985	0.96[ASN][1000 genomes]
rs698992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs699918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs699923	0.96[ASN][1000 genomes]
rs699925	0.96[ASN][1000 genomes]
rs699926	0.96[ASN][1000 genomes]
rs73164102	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166358	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73168723	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73168799	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73170303	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73170306	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73170310	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73170326	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73170337	0.87[EUR][1000 genomes]
rs73170339	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73170346	0.87[EUR][1000 genomes]
rs73170364	0.87[EUR][1000 genomes]
rs73170373	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73170375	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7614572	0.87[JPT][hapmap]
rs7617666	0.81[CEU][hapmap]
rs7622971	0.87[JPT][hapmap]
rs7624303	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7630176	0.86[JPT][hapmap]
rs7640075	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7641036	0.91[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7647342	0.80[JPT][hapmap]
rs7652970	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs827104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs827130	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs827139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs827141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs827142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs827145	0.98[ASN][1000 genomes]
rs827146	0.99[ASN][1000 genomes]
rs827147	0.99[ASN][1000 genomes]
rs827149	0.99[ASN][1000 genomes]
rs827153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs827155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs827157	0.99[ASN][1000 genomes]
rs827160	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs827162	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs827168	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs827170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs827173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs827174	0.89[ASN][1000 genomes]
rs827801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs827805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs860422	0.80[ASN][1000 genomes]
rs862352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs864331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs864876	0.99[ASN][1000 genomes]
rs866657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9290021	0.83[JPT][hapmap]
rs9814942	0.82[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs9881063	1.00[YRI][hapmap]

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	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11717618	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11717618	RP11-538P18.2	cis	Artery Tibial	GTEx
rs11717618	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs11717618	RP11-538P18.2	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157854600-157911800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:157868200-157916200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:157887000-157916400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:157889800-157918600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:157909600-157914200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:157911200-157916400	Weak transcription	Dnd41	blood

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