Variant report

Variant	rs1034617
Chromosome Location	chr7:71701448-71701449
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1015488	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10224695	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10227014	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10227470	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10228688	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10244856	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10248548	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10253915	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10267124	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10277004	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10277561	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10282511	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11762676	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11762805	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11767194	0.90[CEU][hapmap]
rs11971116	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11981237	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1232521	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12539817	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17673971	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2023724	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2023725	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2203709	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2203710	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2677274	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2677277	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2677279	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2677281	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28591449	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28733015	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4719222	0.87[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes]
rs491413	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs492481	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs495016	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs496808	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs501430	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs505671	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs512843	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs520564	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs523703	1.00[CHD][hapmap]
rs531390	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs532169	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs534603	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs536759	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs538657	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs544861	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs549763	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs562477	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62459264	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62464865	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6460710	0.96[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67502107	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6947575	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6962083	0.85[AMR][1000 genomes]
rs6970677	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73143215	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv916220	chr7:71200006-71708048	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1034282	chr7:71531113-71876617	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1015848	chr7:71552185-71736068	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv538942	chr7:71552185-71736068	ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv831024	chr7:71569349-71735250	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv529620	chr7:71604785-71935721	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv492243	chr7:71648955-71935721	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1017911	chr7:71665417-71714246	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv524800	chr7:71666864-71714102	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1019532	chr7:71676605-71714246	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1019700	chr7:71677836-71844973	Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv538943	chr7:71677836-71844973	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1034617	CLDN3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71688400-71709200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:71688600-71714000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:71688800-71702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:71693200-71702800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:71699400-71701800	Weak transcription	Thymus	Thymus
6	chr7:71700400-71705800	Genic enhancers	Fetal Thymus	thymus

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