Variant report

Variant	rs6716842
Chromosome Location	chr2:101066051-101066052
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	chr2:101065530..101068470-chr2:101179201..101180858,2	MCF-7	breast:
2	chr2:101065517..101069142-chr2:101179392..101181432,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115539	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10193824	0.87[AMR][1000 genomes]
rs11690911	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12614705	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12621241	0.83[ASN][1000 genomes]
rs13422218	0.81[MEX][hapmap]
rs1437975	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1437978	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1437980	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1519654	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1519662	0.92[AMR][1000 genomes]
rs17024288	1.00[ASN][1000 genomes]
rs17024457	1.00[JPT][hapmap]
rs2139403	0.81[MEX][hapmap]
rs2176733	0.92[AMR][1000 genomes]
rs2309853	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2309855	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4613309	0.92[AMR][1000 genomes]
rs4850933	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4851322	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851326	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55796343	1.00[ASN][1000 genomes]
rs58553205	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6542952	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542953	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6717716	1.00[CHB][hapmap];0.81[TSI][hapmap]
rs72821202	1.00[ASN][1000 genomes]
rs72823210	0.93[ASN][1000 genomes]
rs72823211	1.00[ASN][1000 genomes]
rs72823215	0.97[ASN][1000 genomes]
rs7369893	0.91[AMR][1000 genomes]
rs7561359	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597493	1.00[JPT][hapmap]
rs7604140	0.83[ASN][1000 genomes]
rs9308836	0.91[AMR][1000 genomes]
rs954846	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs962555	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs962556	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964559	1.00[MEX][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1011990	chr2:101039956-101105648	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6716842	ASTL	cis	parietal	SCAN
rs6716842	C2orf15	cis	parietal	SCAN
rs6716842	MGAT4A	cis	parietal	SCAN
rs6716842	LYG2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101065800-101066400	Active TSS	Pancreas	Pancrea

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