Variant report

Variant	rs6754843
Chromosome Location	chr2:99680485-99680486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99678573..99681466-chr2:99681524..99683363,2	MCF-7	breast:
2	chr2:99678684..99681017-chr2:99686725..99688659,2	MCF-7	breast:
3	chr2:99223859..99226826-chr2:99680320..99683264,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183513	Chromatin interaction
ENSG00000115446	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10164941	0.81[ASN][1000 genomes]
rs10165534	0.80[EUR][1000 genomes]
rs10167390	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170063	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10179043	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs10179910	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10181344	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10181422	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10190421	0.90[CEU][hapmap]
rs1115756	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1115757	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133977	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1133978	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11683107	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11683188	0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11688004	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11692336	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11692669	0.85[ASN][1000 genomes]
rs11895749	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11897712	0.80[CEU][hapmap]
rs11903311	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12053372	0.80[CEU][hapmap]
rs12464710	0.80[EUR][1000 genomes]
rs12467679	0.81[EUR][1000 genomes]
rs12468807	0.90[CEU][hapmap]
rs12470471	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12473029	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs12475034	0.88[CEU][hapmap]
rs12477978	0.87[EUR][1000 genomes]
rs12613624	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12619780	0.97[ASN][1000 genomes]
rs12987548	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13000731	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13008171	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13023501	0.89[ASN][1000 genomes]
rs13033012	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13035357	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13407840	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13412764	0.81[AMR][1000 genomes]
rs1349778	0.90[CEU][hapmap]
rs1349779	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1453561	0.90[CEU][hapmap]
rs1453562	0.90[CEU][hapmap]
rs1453563	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1453564	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1530996	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1563106	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563107	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563108	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1580068	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs17708218	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs17708262	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17759607	1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17760953	0.80[CEU][hapmap]
rs1993230	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2045057	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2084988	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2123686	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2309524	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2516830	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2516833	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2516835	0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2632283	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28575117	0.84[AMR][1000 genomes]
rs28648058	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34272114	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4324365	0.90[CEU][hapmap]
rs4346438	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4347885	0.89[ASN][1000 genomes]
rs4374423	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4585080	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4622780	0.84[CEU][hapmap]
rs4850897	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4851179	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4851183	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851184	0.90[CEU][hapmap]
rs4851185	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4851188	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62154638	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542846	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542866	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6542868	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6704766	0.90[CEU][hapmap]
rs6707462	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6708878	0.89[ASN][1000 genomes]
rs6722164	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6724476	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6727749	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6733285	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6735801	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6736064	0.81[EUR][1000 genomes]
rs6737257	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6740035	0.81[AMR][1000 genomes]
rs6740054	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6750876	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6753650	0.97[ASN][1000 genomes]
rs6756880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6757019	0.90[CEU][hapmap]
rs6759354	0.80[EUR][1000 genomes]
rs720229	1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs72957109	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7558239	0.80[EUR][1000 genomes]
rs7570657	0.83[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7571390	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7586608	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7588059	0.87[ASN][1000 genomes]
rs7591794	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7599427	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7605734	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7606635	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7608938	0.87[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs896886	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs9308816	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9710648	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs972768	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs9808541	0.90[CEU][hapmap]
rs995617	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6754843	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs6754843	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6754843	TSGA10	cis	Lymphoblastoid	GTEx
rs6754843	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6754843	TSGA10	cis	multi-tissue	Pritchard
rs6754843	TSGA10	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99680400-99682400	Weak transcription	Adipose Nuclei	Adipose

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