Variant report

Variant	rs12653370
Chromosome Location	chr5:12507398-12507399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10059816	0.81[ASN][1000 genomes]
rs10474961	0.85[ASN][1000 genomes]
rs10866496	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12652316	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[ASN][1000 genomes]
rs12655048	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12657259	0.83[ASN][1000 genomes]
rs12659112	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16902215	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4339354	0.81[ASN][1000 genomes]
rs4354042	0.84[ASN][1000 genomes]
rs4558988	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs4702885	0.81[ASN][1000 genomes]
rs57357189	0.83[ASN][1000 genomes]
rs59962327	0.83[ASN][1000 genomes]
rs60434293	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60905891	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60926621	0.81[ASN][1000 genomes]
rs6554726	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs6871435	0.83[ASN][1000 genomes]
rs6890802	0.81[ASN][1000 genomes]
rs7700951	0.83[ASN][1000 genomes]
rs7701739	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs7731055	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025096	chr5:12049731-12778382	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537660	chr5:12049731-12778382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1015676	chr5:12276531-12540904	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv427711	chr5:12285375-12747819	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv917255	chr5:12310838-12929427	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv915585	chr5:12336874-12849583	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv880509	chr5:12360373-12778299	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1025123	chr5:12387752-12521009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv537665	chr5:12387752-12521009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv520673	chr5:12389751-12733263	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv880760	chr5:12389751-12921838	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv1016137	chr5:12399805-12521147	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv537666	chr5:12399805-12521147	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv881683	chr5:12401130-12541675	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv817507	chr5:12404458-12902524	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1034539	chr5:12417170-12711376	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1017679	chr5:12457731-13393269	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
18	nsv537667	chr5:12457731-13393269	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
19	nsv880779	chr5:12465904-12525748	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1023259	chr5:12483982-12578638	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1023123	chr5:12488303-12686616	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv1034776	chr5:12502153-12748961	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv537668	chr5:12502153-12748961	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	nsv881461	chr5:12507398-12575182	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12653370	NLRP6	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:12504600-12507400	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr5:12507200-12507400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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