Variant report

Variant	rs2040696
Chromosome Location	chr7:83941201-83941202
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10081337	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10085599	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10231889	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10233152	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10260152	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10263842	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11971807	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1808204	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2214503	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2372167	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35905551	0.81[AMR][1000 genomes]
rs4607535	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs471152	0.85[AMR][1000 genomes]
rs471477	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs488333	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs489440	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs500315	0.83[ASN][1000 genomes]
rs501229	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs512896	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs514083	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs521401	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs537358	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs562475	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs569493	0.86[AMR][1000 genomes]
rs584566	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs585661	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589077	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs592778	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs600346	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs600642	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs614046	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs645226	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6467990	0.82[EUR][1000 genomes]
rs671711	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6946162	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6964607	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6969121	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs726978	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs727784	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7799452	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs812780	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2754468	chr7:83851249-84166749	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1793815	chr7:83909503-83997755	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv524905	chr7:83911271-83944506	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv888631	chr7:83911271-84010005	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2040696	C7orf23	cis	cerebellum	SCAN
rs2040696	KIAA1324L	cis	cerebellum	SCAN
rs2040696	GNAI1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83924400-83943800	Weak transcription	NHDF-Ad	bronchial
2	chr7:83930800-83950000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:83940000-83942400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:83940800-83941400	Active TSS	Rectal Smooth Muscle	rectum
5	chr7:83941200-83941400	Enhancers	Colon Smooth Muscle	Colon

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