Variant report

Variant	rs790829
Chromosome Location	chr5:127036197-127036198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1002214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066288	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10067219	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1067705	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1086479	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1092294	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1213745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13155734	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1356121	0.81[AMR][1000 genomes]
rs1432641	0.81[AMR][1000 genomes]
rs1432642	0.81[AMR][1000 genomes]
rs1464132	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1616107	0.81[AMR][1000 genomes]
rs2673765	0.91[YRI][hapmap]
rs2673770	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34713863	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6867166	0.89[ASW][hapmap]
rs6878186	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs711361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs711362	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs711363	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs711364	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs711366	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs711367	0.80[EUR][1000 genomes]
rs711369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729013	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs790834	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790839	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs790840	0.84[EUR][1000 genomes]
rs790841	0.80[EUR][1000 genomes]
rs796919	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs806464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs810996	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs790829	PRRC1	cis	cerebellum	SCAN
rs790829	CTXN3	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127032800-127040800	Weak transcription	NHDF-Ad	bronchial
2	chr5:127033000-127038400	Weak transcription	Psoas Muscle	Psoas
3	chr5:127033000-127040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:127033000-127040600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:127033000-127041000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:127033800-127040600	Weak transcription	NHLF	lung
7	chr5:127034200-127037800	Weak transcription	Left Ventricle	heart
8	chr5:127034200-127038200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:127034200-127038400	Weak transcription	Right Atrium	heart
10	chr5:127034200-127040800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:127034200-127041000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:127034800-127036200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:127035200-127036400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:127035200-127036600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:127035200-127036600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:127035600-127036800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:127035800-127039000	Weak transcription	A549	lung
18	chr5:127035800-127040600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:127035800-127041000	Weak transcription	Fetal Lung	lung
20	chr5:127035800-127041200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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