Variant report

Variant	rs1530996
Chromosome Location	chr2:99584079-99584080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10165534	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10170063	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10179043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs10181344	0.90[CEU][hapmap]
rs10181422	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10190421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs10193019	0.86[EUR][1000 genomes]
rs10193113	0.83[EUR][1000 genomes]
rs10196680	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10202452	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865029	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11123761	1.00[CHB][hapmap];0.80[YRI][hapmap]
rs11123765	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1115756	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1115757	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11677247	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11692699	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11695379	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11695751	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11897712	0.85[CEU][hapmap]
rs11900670	0.83[AFR][1000 genomes]
rs12464710	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12467679	0.89[EUR][1000 genomes]
rs12468807	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12470471	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12473029	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12475034	0.94[CEU][hapmap]
rs12477754	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12477978	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12995473	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs13008496	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs13018891	1.00[CHB][hapmap];0.97[YRI][hapmap]
rs13035311	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs13396358	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13407840	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13412764	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13422604	0.81[EUR][1000 genomes]
rs1349778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs1349779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1453561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap]
rs1453562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1453564	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1580068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17708218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17708262	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1993230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2045057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2084988	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2123686	0.90[CEU][hapmap]
rs2309524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2516827	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2516829	1.00[CHB][hapmap];0.80[YRI][hapmap]
rs2516832	1.00[CHB][hapmap]
rs2516834	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2632260	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2632277	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs28575117	0.84[AMR][1000 genomes]
rs28648058	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35001733	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4324365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4340581	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4346438	0.83[EUR][1000 genomes]
rs4374423	0.90[CEU][hapmap]
rs4585080	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4588238	1.00[CHB][hapmap];0.96[YRI][hapmap]
rs4622780	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs4851179	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851183	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4851185	0.90[CEU][hapmap]
rs4851187	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs62154638	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62156558	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6542846	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6542852	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6542858	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6542864	1.00[CHB][hapmap];0.96[YRI][hapmap]
rs6542865	1.00[CHB][hapmap];0.97[YRI][hapmap]
rs6704766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6717723	1.00[CHB][hapmap];0.97[YRI][hapmap]
rs6717729	1.00[CHB][hapmap];0.93[YRI][hapmap]
rs6721535	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6722164	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6724476	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6732579	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735801	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6736064	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6737257	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6740035	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6740054	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6740267	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741772	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs6750876	0.90[CEU][hapmap]
rs6751927	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6753650	0.81[AFR][1000 genomes]
rs6754843	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6756880	0.90[CEU][hapmap]
rs6757019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6759354	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs720228	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs72957109	0.80[EUR][1000 genomes]
rs7558239	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7570657	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7571390	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7577477	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7586608	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7591794	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7599427	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7605734	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7606635	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs896886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9308816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9710648	0.90[CEU][hapmap]
rs972768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9808541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9941561	1.00[CHB][hapmap]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1530996	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs1530996	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs1530996	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs1530996	TSGA10	cis	Lymphoblastoid	GTEx
rs1530996	TSGA10	cis	multi-tissue	Pritchard
rs1530996	TSGA10	cis	Thyroid	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99583400-99584200	ZNF genes & repeats	Gastric	stomach
2	chr2:99583400-99584200	ZNF genes & repeats	Pancreas	Pancrea
3	chr2:99583800-99584200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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