Variant report

Variant	rs7722926
Chromosome Location	chr5:147286013-147286014
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10477355	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1123380	0.81[YRI][hapmap]
rs11958481	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1432973	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432974	0.83[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1549204	0.82[ASW][hapmap];0.82[LWK][hapmap];0.92[YRI][hapmap]
rs17107413	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17107421	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17703848	0.85[CEU][hapmap]
rs1835968	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1835969	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2304067	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6580506	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580507	0.85[EUR][1000 genomes]
rs6859879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862197	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73263247	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7706789	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7708635	0.88[YRI][hapmap]
rs7709303	0.82[ASW][hapmap];0.82[LWK][hapmap];0.88[YRI][hapmap]
rs7722416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv520730	chr5:147285713-147286054	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7722926	SCGB3A2	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147273400-147289000	Weak transcription	Left Ventricle	heart
2	chr5:147283400-147286800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:147283600-147286800	Enhancers	HMEC	breast
4	chr5:147284000-147286200	Active TSS	Aorta	Aorta
5	chr5:147284000-147286400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:147284200-147291000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:147285000-147286200	Active TSS	Right Ventricle	heart
8	chr5:147285000-147286800	Enhancers	Fetal Heart	heart
9	chr5:147285400-147286800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:147285600-147286800	Enhancers	Hela-S3	cervix
11	chr5:147285800-147286200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:147285800-147286200	Flanking Active TSS	NH-A	brain
13	chr5:147285800-147286200	Flanking Active TSS	Osteobl	bone
14	chr5:147285800-147286600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:147285800-147286600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:147285800-147286600	Enhancers	HSMM	muscle
17	chr5:147285800-147286800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:147285800-147286800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:147285800-147286800	Enhancers	Placenta	Placenta
20	chr5:147286000-147286200	Enhancers	Right Atrium	heart
21	chr5:147286000-147286200	Enhancers	Stomach Mucosa	stomach
22	chr5:147286000-147286200	Flanking Active TSS	HSMMtube	muscle
23	chr5:147286000-147286600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:147286000-147286600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:147286000-147286600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:147286000-147286600	Enhancers	Gastric	stomach
27	chr5:147286000-147286600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr5:147286000-147286600	Flanking Active TSS	NHEK	skin
29	chr5:147286000-147286800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:147286000-147286800	Enhancers	Pancreas	Pancrea

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