Variant report

Variant	rs12039053
Chromosome Location	chr1:155923876-155923877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155923583-155923910	U87	brain:	n/a	n/a
2	POLR2A	chr1:155923568-155923908	K562	blood:	n/a	n/a
3	POLR2A	chr1:155923583-155923887	U87	brain:	n/a	n/a
4	POLR2A	chr1:155923484-155923890	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155904710..155906723-chr1:155922247..155924795,2	K562	blood:
2	chr1:155909425..155917901-chr1:155919093..155927049,14	K562	blood:
3	chr1:155910464..155913363-chr1:155922030..155924734,3	K562	blood:

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000173080	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1010033	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1018730	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1055184	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908485	0.97[EUR][1000 genomes]
rs1094558	0.83[AFR][1000 genomes]
rs11264421	0.92[EUR][1000 genomes]
rs12129384	0.94[AFR][1000 genomes]
rs12138833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747344	0.99[EUR][1000 genomes]
rs1749407	0.89[EUR][1000 genomes]
rs1749408	0.84[EUR][1000 genomes]
rs1749409	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1765275	0.97[EUR][1000 genomes]
rs1964951	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2275071	1.00[ASN][1000 genomes]
rs2275079	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275081	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364404	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34802187	0.99[EUR][1000 genomes]
rs35138477	0.85[EUR][1000 genomes]
rs35374730	0.96[EUR][1000 genomes]
rs35588936	0.85[EUR][1000 genomes]
rs35730001	0.96[EUR][1000 genomes]
rs3738587	0.81[ASN][1000 genomes]
rs3768280	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4412586	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4661160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661162	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661170	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4661172	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493446	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506688	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs527113	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536870	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs572609	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605025	0.97[EUR][1000 genomes]
rs6660802	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667096	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs708614	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71628697	0.97[EUR][1000 genomes]
rs71628699	0.86[EUR][1000 genomes]
rs822502	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs822503	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs822653	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155911200-155940000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155914800-155929600	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr1:155914800-155929800	Strong transcription	Fetal Stomach	stomach
5	chr1:155914800-155930200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:155914800-155931600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:155915200-155927400	Strong transcription	Brain Anterior Caudate	brain
8	chr1:155915200-155930600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:155915200-155936800	Strong transcription	Fetal Brain Female	brain
10	chr1:155915200-155937000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:155915800-155925400	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr1:155915800-155929600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:155915800-155929600	Strong transcription	HMEC	breast
14	chr1:155915800-155929800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:155915800-155929800	Strong transcription	HSMMtube	muscle
16	chr1:155915800-155930000	Strong transcription	Left Ventricle	heart
17	chr1:155915800-155930400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:155915800-155930400	Strong transcription	Osteobl	bone
19	chr1:155915800-155930600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:155915800-155931600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:155915800-155935200	Strong transcription	Brain Germinal Matrix	brain
22	chr1:155915800-155936600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:155916000-155925400	Strong transcription	Gastric	stomach
24	chr1:155916000-155925400	Strong transcription	NHEK	skin
25	chr1:155916000-155926000	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr1:155916000-155930600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:155916000-155931400	Strong transcription	HUVEC	blood vessel
28	chr1:155916000-155937000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:155916200-155925400	Strong transcription	K562	blood
30	chr1:155916200-155926000	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr1:155916200-155929800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:155916200-155929800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:155916200-155930200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:155916200-155931600	Weak transcription	Right Atrium	heart
35	chr1:155916200-155932400	Strong transcription	Colon Smooth Muscle	Colon
36	chr1:155916200-155937000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:155916400-155926000	Strong transcription	Fetal Lung	lung
38	chr1:155916400-155929000	Strong transcription	Placenta	Placenta
39	chr1:155916400-155929400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr1:155916400-155930400	Strong transcription	Adipose Nuclei	Adipose
41	chr1:155916400-155930600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:155916400-155931800	Strong transcription	Lung	lung
43	chr1:155916400-155936200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:155916400-155936400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr1:155916400-155936600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:155916400-155937200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:155916400-155937400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:155916600-155930000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:155916600-155932400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:155916600-155935800	Strong transcription	Fetal Intestine Small	intestine

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