Variant report

Variant	rs3797513
Chromosome Location	chr5:106729992-106729993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11242636	1.00[CEU][hapmap]
rs11956440	1.00[CEU][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap]
rs13178242	0.88[CEU][hapmap];0.86[CHD][hapmap]
rs13182976	1.00[CEU][hapmap];0.86[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs35021422	0.81[EUR][1000 genomes]
rs3756544	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3797510	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797514	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3797516	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3797517	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3797521	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs3797527	0.88[CEU][hapmap]
rs3873122	1.00[CEU][hapmap]
rs3901010	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs59863014	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66505151	0.81[EUR][1000 genomes]
rs6868410	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs72785812	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72785815	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72785816	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72785818	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7703776	1.00[CEU][hapmap]

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	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3797513	FAM36A	trans	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106720400-106740800	Weak transcription	Aorta	Aorta
2	chr5:106723600-106732000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:106724200-106730200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:106725200-106730000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:106725200-106733800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:106725600-106732200	Weak transcription	Left Ventricle	heart
7	chr5:106725800-106730200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:106725800-106731200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:106725800-106731800	Weak transcription	Osteobl	bone
10	chr5:106725800-106732000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:106725800-106732000	Weak transcription	Fetal Heart	heart
12	chr5:106725800-106732400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:106725800-106740400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:106726000-106730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:106726000-106730000	Weak transcription	Stomach Mucosa	stomach
16	chr5:106726000-106731000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:106726000-106731400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:106726000-106731400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:106728000-106730600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:106728200-106730200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:106728200-106730600	Enhancers	NHDF-Ad	bronchial
22	chr5:106728400-106732200	Weak transcription	Ovary	ovary
23	chr5:106728400-106732600	Enhancers	A549	lung
24	chr5:106728400-106738200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:106728600-106731400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:106728600-106733600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:106729200-106730000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:106729400-106730000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:106729400-106730000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:106729400-106730000	Enhancers	NHLF	lung
31	chr5:106729400-106731600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr5:106729400-106732400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:106729600-106730000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:106729600-106730000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:106729600-106730000	Enhancers	Fetal Lung	lung
36	chr5:106729600-106730800	Enhancers	Fetal Kidney	kidney
37	chr5:106729600-106732800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr5:106729800-106730000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:106729800-106730200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr5:106729800-106730400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:106729800-106731000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:106729800-106731400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:106729800-106733000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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