Variant report

Variant	rs7515157
Chromosome Location	chr1:171179477-171179478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158051	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912619	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912661	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3174837	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35434145	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916269	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425286	0.90[ASN][1000 genomes]
rs7512785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516374	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7542248	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7545153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551531	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1817255	chr1:171170733-171185865	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7515157	FMO2	cis	cerebellum	SCAN
rs7515157	FMO2	cis	Artery Tibial	GTEx
rs7515157	RCSD1	cis	cerebellum	SCAN
rs7515157	FMO2	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171156600-171179600	Weak transcription	NHLF	lung
2	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
3	chr1:171166000-171184000	Weak transcription	Gastric	stomach
4	chr1:171167200-171187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:171169800-171189800	Weak transcription	Right Atrium	heart
6	chr1:171177800-171183600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:171178000-171183200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:171178200-171180800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:171178200-171182600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:171178200-171187200	Weak transcription	Aorta	Aorta
11	chr1:171178600-171179800	Enhancers	Liver	Liver
12	chr1:171178600-171181000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:171178600-171181600	Enhancers	Adipose Nuclei	Adipose
14	chr1:171178600-171182800	Weak transcription	Left Ventricle	heart
15	chr1:171178800-171179600	Enhancers	Stomach Mucosa	stomach
16	chr1:171178800-171180600	Enhancers	Fetal Intestine Large	intestine
17	chr1:171179000-171179600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:171179000-171179600	Enhancers	Duodenum Mucosa	Duodenum
19	chr1:171179000-171179800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:171179000-171179800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:171179000-171180600	Enhancers	Fetal Intestine Small	intestine
22	chr1:171179200-171179600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:171179200-171179800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:171179200-171180600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:171179200-171180600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:171179400-171179600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr1:171179400-171179800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr1:171179400-171179800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:171179400-171179800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:171179400-171179800	Enhancers	Brain Substantia Nigra	brain
31	chr1:171179400-171179800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr1:171179400-171179800	Enhancers	Fetal Kidney	kidney
33	chr1:171179400-171180000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:171179400-171180200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:171179400-171180600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr1:171179400-171180600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:171179400-171181000	Enhancers	Fetal Lung	lung

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