Variant report

Variant	rs682964
Chromosome Location	chr1:86448864-86448865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10732722	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10782562	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1112326	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1112327	0.93[CHB][hapmap]
rs11161709	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161710	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161711	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12144570	0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12740695	0.82[CHB][hapmap]
rs1354245	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1359421	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1481201	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1481202	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1502657	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1604568	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1698733	0.93[CHB][hapmap]
rs4303095	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4486475	0.93[CHB][hapmap]
rs474832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs482981	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486726	0.87[CHB][hapmap]
rs489141	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518829	0.85[ASN][1000 genomes]
rs532186	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs559247	0.93[CHB][hapmap]
rs560876	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs571691	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs578615	0.87[CHB][hapmap]
rs589698	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs597330	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs603297	0.93[CHB][hapmap]
rs605060	0.93[CHB][hapmap]
rs631632	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs647977	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673508	0.93[CHB][hapmap]
rs6699709	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6702912	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs686272	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512136	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7512890	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7524896	0.87[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541806	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs861933	0.93[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462395	chr1:86379514-86457334	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv546726	chr1:86379514-86457334	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546758	chr1:86438327-86483632	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3340591	chr1:86439980-86459810	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs682964	CLCA4	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86446200-86450800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:86447800-86450000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:86448200-86449000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:86448600-86449800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:86448600-86452800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:86448800-86449000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:86448800-86449000	Enhancers	Fetal Lung	lung
8	chr1:86448800-86449000	Enhancers	GM12878-XiMat	blood
9	chr1:86448800-86451200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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