Variant report

Variant	rs7757409
Chromosome Location	chr6:58768721-58768722
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2880516	0.92[ASN][1000 genomes]
rs6588714	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9500405	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523720	chr6:58075480-58770624	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1024377	chr6:58082084-58774716	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1020262	chr6:58140288-58774716	ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2760987	chr6:58140300-58774716	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking 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
5	nsv1017058	chr6:58165571-58774716	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv603237	chr6:58231219-58780055	Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
7	nsv462957	chr6:58285920-58770624	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv603239	chr6:58285920-58770624	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1032012	chr6:58376124-58774716	Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019783	chr6:58409674-58774716	ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1033773	chr6:58447068-58774716	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv427758	chr6:58502261-58780166	ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
13	nsv1019258	chr6:58547058-58774716	ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv603241	chr6:58567162-58775043	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv469832	chr6:58612801-58773702	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv482772	chr6:58612801-58773702	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1024371	chr6:58613247-58774716	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv1025649	chr6:58653250-58774716	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv1022731	chr6:58657502-58774716	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv1028174	chr6:58661362-58774716	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv1028725	chr6:58662879-58774716	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv1034815	chr6:58669656-58774716	ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1031194	chr6:58681762-58774716	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv1024021	chr6:58700635-58774716	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv1033411	chr6:58707568-58774716	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	esv13666	chr6:58714399-58773619	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv527572	chr6:58714937-58770624	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
28	nsv1034225	chr6:58718659-58774716	ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
29	nsv603242	chr6:58754939-58776198	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
30	nsv603243	chr6:58754939-58779628	Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7757409	LINC00680	cis	Artery Tibial	GTEx
rs7757409	LINC00680	cis	Thyroid	GTEx
rs7757409	LINC00680	cis	Muscle Skeletal	GTEx
rs7757409	XXbac-BPGBPG55C20.2	cis	Artery Tibial	GTEx
rs7757409	LINC00680	cis	lung	GTEx
rs7757409	LINC00680	cis	Whole Blood	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:58765200-58769400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:58768000-58771000	ZNF genes & repeats	Liver	Liver

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