Variant report

Variant	rs3789453
Chromosome Location	chr1:94374026-94374027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94337226..94339966-chr1:94373816..94376815,2	K562	blood:
2	chr1:94372270..94376088-chr1:94480112..94484516,4	K562	blood:
3	chr1:94312303..94314752-chr1:94373572..94376301,2	MCF-7	breast:
4	chr1:94344173..94346291-chr1:94372636..94375124,3	K562	blood:
5	chr1:94343199..94347658-chr1:94372955..94376562,9	MCF-7	breast:
6	chr1:94344690..94346304-chr1:94373768..94376372,3	MCF-7	breast:
7	chr1:93811453..93814121-chr1:94372637..94375148,3	K562	blood:
8	chr1:94350854..94353775-chr1:94372233..94374131,2	K562	blood:
9	chr1:93811453..93813762-chr1:94372603..94376116,3	K562	blood:
10	chr1:94342014..94348814-chr1:94369991..94376733,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000223745	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000117505	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000198691	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000260464	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1473712	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473713	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1884019	0.83[GIH][hapmap];0.94[JPT][hapmap]
rs2064765	0.88[ASN][1000 genomes]
rs2143991	0.84[EUR][1000 genomes]
rs2144872	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144873	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301022	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747042	0.80[GIH][hapmap];0.94[JPT][hapmap]
rs3789457	0.87[CEU][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs4427413	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4520428	0.83[GIH][hapmap]
rs4578232	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847257	0.83[GIH][hapmap]
rs4847268	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6660210	0.83[GIH][hapmap];0.94[JPT][hapmap]
rs6679978	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6683813	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6703130	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs743110	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs743112	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7523787	0.94[JPT][hapmap]
rs7526082	0.85[EUR][1000 genomes]
rs7526920	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552293	0.83[GIH][hapmap];0.94[JPT][hapmap]
rs9725707	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs990576	0.84[AMR][1000 genomes];0.88[ASN][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	nsv523355	chr1:94351328-94385591	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3404764	chr1:94372564-94377162	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3426478	chr1:94373589-94376737	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3789453	ALG14	cis	cerebellum	SCAN
rs3789453	GEMIN8P4	cis	cerebellum	SCAN
rs3789453	GCLM	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94345000-94374200	Weak transcription	Gastric	stomach
2	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
3	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:94347400-94374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94357600-94374200	Weak transcription	Pancreas	Pancrea
6	chr1:94362600-94374200	Weak transcription	Left Ventricle	heart
7	chr1:94369600-94375800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:94370800-94375200	Active TSS	HMEC	breast
9	chr1:94371200-94375200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:94371600-94374400	Flanking Active TSS	Liver	Liver
11	chr1:94372400-94374400	Flanking Active TSS	Dnd41	blood
12	chr1:94372400-94375800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:94372400-94375800	Active TSS	NHLF	lung
14	chr1:94372600-94374400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:94372800-94376000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:94373000-94374200	Flanking Active TSS	Hela-S3	cervix
17	chr1:94373000-94374400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:94373000-94374400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr1:94373000-94374400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr1:94373200-94374200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:94373200-94374200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:94373200-94374200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
23	chr1:94373200-94374200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:94373200-94374200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:94373200-94374200	Enhancers	Esophagus	oesophagus
26	chr1:94373200-94374200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:94373200-94374400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:94373200-94375600	Active TSS	Brain Angular Gyrus	brain
29	chr1:94373200-94375800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:94373400-94374200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
31	chr1:94373400-94374200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr1:94373400-94374200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:94373400-94374400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:94373400-94374400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:94373400-94374400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:94373400-94374400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr1:94373400-94374600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:94373400-94374600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:94373400-94375800	Active TSS	H9 Cell Line	embryonic stem cell
40	chr1:94373400-94375800	Active TSS	HSMMtube	muscle
41	chr1:94373600-94374200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:94373600-94374200	Enhancers	Primary B cells from peripheral blood	blood
43	chr1:94373600-94374400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:94373600-94374400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:94373600-94375400	Active TSS	H1 Cell Line	embryonic stem cell
46	chr1:94373600-94375400	Active TSS	K562	blood
47	chr1:94373600-94375600	Active TSS	Psoas Muscle	Psoas
48	chr1:94373600-94375600	Active TSS	A549	lung
49	chr1:94373600-94375600	Active TSS	HepG2	liver
50	chr1:94373600-94375800	Active TSS	NHDF-Ad	bronchial

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