Variant report

Variant	rs36055753
Chromosome Location	chr1:227464748-227464749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11800169	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801282	0.87[EUR][1000 genomes]
rs11803651	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806721	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11807068	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11807375	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11807425	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11807957	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11808210	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11808670	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11808674	0.89[EUR][1000 genomes]
rs11809113	0.81[AFR][1000 genomes]
rs11809905	0.89[EUR][1000 genomes]
rs11811620	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11812048	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35601687	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41270147	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6671926	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7524967	0.81[AFR][1000 genomes]
rs7530155	0.91[EUR][1000 genomes]
rs7547092	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9660532	0.82[AMR][1000 genomes];0.91[EUR][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3453491	chr1:227462942-227482283	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3453492	chr1:227462956-227482280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs36055753	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
2	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
3	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:227449600-227473600	Weak transcription	NH-A	brain
7	chr1:227449800-227465200	Weak transcription	K562	blood
8	chr1:227453000-227468600	Weak transcription	Lung	lung
9	chr1:227454200-227470400	Weak transcription	Ovary	ovary
10	chr1:227456600-227468800	Weak transcription	Left Ventricle	heart
11	chr1:227458600-227469400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:227458800-227472200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:227459400-227469400	Weak transcription	NHEK	skin
14	chr1:227459600-227465800	Weak transcription	A549	lung
15	chr1:227461800-227465000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:227462600-227473600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:227463000-227473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:227463800-227464800	Weak transcription	Brain Substantia Nigra	brain
20	chr1:227464400-227468000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:227464400-227469000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:227464400-227472800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:227464400-227472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:227464600-227468600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:227464600-227468600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:227464600-227469400	Weak transcription	Gastric	stomach

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