Variant report

Variant	rs4719141
Chromosome Location	chr7:71003462-71003463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10224027	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10235508	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10237318	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10242031	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10244344	0.82[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs10447533	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs11763708	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11769266	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773571	0.81[CHB][hapmap]
rs28658503	0.95[ASN][1000 genomes]
rs28709000	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4128374	0.83[YRI][hapmap]
rs4557585	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4717604	0.81[CHB][hapmap]
rs4719140	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719142	0.98[ASN][1000 genomes]
rs55780804	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56230426	0.86[ASN][1000 genomes]
rs56268443	0.86[ASN][1000 genomes]
rs58587487	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59543111	0.95[ASN][1000 genomes]
rs60560541	0.85[ASN][1000 genomes]
rs62459927	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62459931	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62459956	0.95[ASN][1000 genomes]
rs6460664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs6460669	0.83[YRI][hapmap]
rs6460670	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460671	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460673	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460674	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6960915	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6973274	0.96[ASN][1000 genomes]
rs6977973	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7777634	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779947	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7786397	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7788004	0.86[ASN][1000 genomes]
rs7799605	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7803346	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7805159	0.94[ASN][1000 genomes]
rs7806531	0.83[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1033783	chr7:70955277-71023877	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4719141	CLDN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70983000-71007800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:70986800-71006600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:70988000-71023800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:71002000-71006600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:71003400-71003600	Enhancers	Fetal Lung	lung
6	chr7:71003400-71004000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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