Variant report

Variant	rs17123220
Chromosome Location	chr1:62703686-62703687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10493319	1.00[CEU][hapmap]
rs17123225	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56908498	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74079050	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17123220	ECAT11	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62697000-62706600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:62698200-62704000	Enhancers	NHEK	skin
3	chr1:62698600-62704400	Enhancers	Hela-S3	cervix
4	chr1:62699000-62706600	Weak transcription	Fetal Lung	lung
5	chr1:62699000-62706800	Weak transcription	Pancreas	Pancrea
6	chr1:62699800-62704200	Enhancers	HMEC	breast
7	chr1:62700000-62704000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:62700400-62704000	Enhancers	HSMM	muscle
9	chr1:62700800-62703800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:62701000-62707400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:62701000-62710800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:62701400-62709400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:62701600-62704200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:62701600-62704200	Enhancers	HSMMtube	muscle
15	chr1:62701600-62705000	Enhancers	HepG2	liver
16	chr1:62702000-62704000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:62702000-62704200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:62702200-62706800	Weak transcription	Liver	Liver
19	chr1:62702800-62703800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:62702800-62703800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:62702800-62704000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr1:62702800-62704000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr1:62702800-62704200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:62702800-62704400	Enhancers	A549	lung
25	chr1:62703000-62704000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr1:62703200-62704000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr1:62703200-62704000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr1:62703200-62704200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:62703200-62704400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:62703400-62704000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:62703400-62704000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:62703400-62704200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr1:62703400-62704200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:62703400-62704200	Strong transcription	Adipose Nuclei	Adipose
35	chr1:62703400-62704200	Enhancers	Placenta	Placenta
36	chr1:62703400-62704400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:62703600-62703800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr1:62703600-62703800	Enhancers	Fetal Kidney	kidney
39	chr1:62703600-62704000	Enhancers	Fetal Heart	heart
40	chr1:62703600-62704000	Genic enhancers	Fetal Stomach	stomach
41	chr1:62703600-62704200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:62703600-62704200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr1:62703600-62704200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:62703600-62704200	Genic enhancers	Fetal Muscle Leg	muscle
45	chr1:62703600-62704600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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