Variant report

Variant	rs1561522
Chromosome Location	chr2:35823374-35823375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10168316	0.96[ASN][1000 genomes]
rs10191383	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10200498	0.92[ASN][1000 genomes]
rs11124450	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11124451	0.88[ASN][1000 genomes]
rs11678496	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13015441	0.94[ASN][1000 genomes]
rs1371417	0.95[ASN][1000 genomes]
rs1371419	0.80[EUR][1000 genomes]
rs1439686	0.93[ASN][1000 genomes]
rs1595729	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898934	0.98[ASN][1000 genomes]
rs1898935	0.95[ASN][1000 genomes]
rs1898939	0.95[ASN][1000 genomes]
rs2028345	0.92[ASN][1000 genomes]
rs2043914	0.96[ASN][1000 genomes]
rs2372008	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2719091	0.81[EUR][1000 genomes]
rs2719093	0.81[EUR][1000 genomes]
rs4398250	0.89[ASN][1000 genomes]
rs4410271	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4578836	0.92[ASN][1000 genomes]
rs7425548	0.97[ASN][1000 genomes]
rs7562305	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9308973	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9308974	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs934970	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs934971	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010722	chr2:35072575-35950219	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv519522	chr2:35425529-35861883	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1008651	chr2:35469467-35896486	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv999139	chr2:35483033-35860024	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv535636	chr2:35483033-35860024	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873848	chr2:35641532-35973963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949472	chr2:35709203-36447481	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1009123	chr2:35728920-36412880	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv535639	chr2:35728920-36412880	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv998313	chr2:35731937-36422991	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv535640	chr2:35731937-36422991	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv2674	chr2:35800855-35845742	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	nsv581403	chr2:35813328-35844915	ZNF genes & repeats Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases
14	nsv873850	chr2:35814079-35985118	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv873851	chr2:35814079-36095438	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1011694	chr2:35815793-36089929	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv470452	chr2:35818106-36087642	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv873852	chr2:35818107-35926513	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv581404	chr2:35818107-36079256	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv519867	chr2:35818107-36087642	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv581405	chr2:35818107-36087642	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv873853	chr2:35818107-36095438	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1014685	chr2:35818922-36088630	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv1002300	chr2:35818922-36089472	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv1001058	chr2:35818922-36089929	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	esv2763629	chr2:35818934-36092158	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv430690	chr2:35818997-36085649	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv833759	chr2:35821360-35983782	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv996311	chr2:35821806-36061904	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv915880	chr2:35821820-36061990	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
31	nsv1010615	chr2:35822856-36088630	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1561522	GEMIN6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:35823200-35826000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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