Variant report

Variant	rs248695
Chromosome Location	chr5:126999493-126999494
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10072627	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1086482	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1123820	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1228885	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13182486	0.96[CEU][hapmap]
rs2138273	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248693	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248697	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248699	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs248704	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248708	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248714	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248719	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs248723	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs248725	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs248727	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs248728	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs248729	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs248734	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2569143	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2673751	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2673762	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs790832	0.81[ASN][1000 genomes]
rs790833	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs790835	0.83[ASN][1000 genomes]
rs790837	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv830479	chr5:126849254-127053121	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv599664	chr5:126974071-127016256	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs248695	SLC12A2	cis	cerebellum	SCAN
rs248695	CTXN3	cis	parietal	SCAN
rs248695	FBN2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126991400-127001800	Weak transcription	Fetal Lung	lung
2	chr5:126996000-127000000	Weak transcription	Psoas Muscle	Psoas
3	chr5:126996200-127002200	Weak transcription	Fetal Stomach	stomach
4	chr5:126996200-127006200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:126996400-126999800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:126996400-127001800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:126996400-127002200	Weak transcription	Left Ventricle	heart
8	chr5:126996400-127006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:126996600-127001400	Weak transcription	Fetal Heart	heart
10	chr5:126996600-127001800	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:126997600-127001800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:126998800-127000800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:126998800-127001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:126999000-127000200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:126999000-127000600	Enhancers	Ovary	ovary

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