Variant report

Variant	rs6958460
Chromosome Location	chr7:66854416-66854417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10224468	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10249620	0.90[EUR][1000 genomes]
rs10273547	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045513	0.80[JPT][hapmap]
rs10950071	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11765153	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11765818	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11767326	0.87[EUR][1000 genomes]
rs11771384	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11970911	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11976633	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11983916	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12112805	0.89[EUR][1000 genomes]
rs12698579	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12698581	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12698582	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12698583	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12698586	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318091	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1989425	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017343	0.91[EUR][1000 genomes]
rs2017374	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2041575	0.80[JPT][hapmap]
rs2604420	0.86[ASN][1000 genomes]
rs34000470	0.95[ASN][1000 genomes]
rs36108509	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4717369	0.86[ASN][1000 genomes]
rs4717375	0.91[EUR][1000 genomes]
rs4717377	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4717378	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718532	0.94[ASN][1000 genomes]
rs4718533	0.94[ASN][1000 genomes]
rs4718535	0.94[ASN][1000 genomes]
rs4718539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718544	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718545	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718546	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718547	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718548	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718549	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718550	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4718551	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62467569	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62467571	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460340	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6947353	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6963760	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967594	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979307	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759012	0.94[ASN][1000 genomes]
rs759013	0.94[ASN][1000 genomes]
rs7788614	0.85[EUR][1000 genomes]
rs7791024	0.80[JPT][hapmap]
rs7806514	0.92[ASN][1000 genomes]
rs887710	0.94[ASN][1000 genomes]
rs985435	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1031147	chr7:66811313-66922350	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1025049	chr7:66823977-66906930	Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6958460	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs6958460	STAG3L4	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66853800-66857400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:66854200-66855000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:66854400-66854600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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