Variant report

Variant	rs7429544
Chromosome Location	chr3:75285488-75285489
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12486094	0.83[MEX][hapmap]
rs12488229	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs12491189	0.87[ASN][1000 genomes]
rs28449831	0.88[ASN][1000 genomes]
rs35847359	0.83[ASN][1000 genomes]
rs4072316	0.86[ASN][1000 genomes]
rs4298064	0.80[ASN][1000 genomes]
rs4613477	0.82[ASN][1000 genomes]
rs56711387	0.86[ASN][1000 genomes]
rs58346667	0.87[ASN][1000 genomes]
rs59738586	0.82[ASN][1000 genomes]
rs62261024	0.87[ASN][1000 genomes]
rs62261027	0.86[ASN][1000 genomes]
rs62261028	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62261034	0.86[ASN][1000 genomes]
rs62261035	0.82[ASN][1000 genomes]
rs62261037	0.82[EUR][1000 genomes]
rs62261038	0.84[ASN][1000 genomes]
rs62261042	0.85[ASN][1000 genomes]
rs62261043	0.82[ASN][1000 genomes]
rs62261046	0.80[ASN][1000 genomes]
rs7428379	0.82[ASN][1000 genomes]
rs7428818	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430900	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7433238	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529994	chr3:74720752-75471887	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv916594	chr3:74943399-75540161	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv997253	chr3:75168497-76021627	Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv876961	chr3:75193473-75331002	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv876962	chr3:75198904-75540544	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
6	nsv876963	chr3:75202547-75331002	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv876964	chr3:75202547-75437889	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1002218	chr3:75221611-75702475	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
9	nsv876965	chr3:75222937-75294417	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv460704	chr3:75228373-75322243	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	nsv590641	chr3:75228373-75322243	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
12	esv2422240	chr3:75244279-75595933	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
13	nsv432427	chr3:75249409-75676582	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
14	esv2422315	chr3:75250088-75853296	Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
15	nsv432428	chr3:75269488-75697169	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7429544	ZNF717	cis	cerebellum	SCAN
rs7429544	FAM86DP	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:75284600-75286600	Enhancers	H9 Cell Line	embryonic stem cell
2	chr3:75285000-75286200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:75285000-75287200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:75285200-75285600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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