Variant report

Variant	rs2889539
Chromosome Location	chr1:226328740-226328741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226321369..226323954-chr1:226327416..226330476,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10732276	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799337	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799340	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10915952	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10915953	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12032630	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12047894	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2306121	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3914142	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653718	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653722	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9286997	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9286998	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9659225	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9659397	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9660696	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9660874	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9660924	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9661836	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9662709	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9725308	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9725342	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9728014	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9728310	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9729232	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9729554	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2889539	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
2	chr1:226310800-226331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:226317200-226331200	Weak transcription	Placenta	Placenta
4	chr1:226318600-226331600	Weak transcription	NH-A	brain
5	chr1:226319600-226331200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:226320800-226334000	Weak transcription	K562	blood
7	chr1:226321000-226331000	Weak transcription	HSMM	muscle
8	chr1:226321200-226331800	Weak transcription	HSMMtube	muscle
9	chr1:226321400-226331600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:226321400-226331600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:226321400-226331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:226321400-226333800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:226321400-226333800	Weak transcription	GM12878-XiMat	blood
14	chr1:226321800-226331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:226322000-226331600	Weak transcription	Primary B cells from cord blood	blood
16	chr1:226322000-226334400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:226322200-226331600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:226322200-226331800	Weak transcription	HMEC	breast
19	chr1:226322800-226333000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:226323200-226330600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:226323200-226331200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:226323200-226331800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:226323200-226331800	Weak transcription	Spleen	Spleen
24	chr1:226323200-226333200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:226323200-226333600	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:226323200-226333800	Weak transcription	A549	lung
27	chr1:226323200-226334400	Weak transcription	NHEK	skin
28	chr1:226323200-226344600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:226323400-226329600	Weak transcription	Right Atrium	heart
30	chr1:226323400-226331000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:226323400-226331000	Weak transcription	Adipose Nuclei	Adipose
32	chr1:226323400-226331600	Weak transcription	Fetal Thymus	thymus
33	chr1:226323400-226331600	Weak transcription	Osteobl	bone
34	chr1:226323400-226331800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:226323400-226331800	Weak transcription	Left Ventricle	heart
36	chr1:226323400-226338400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:226323600-226330800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:226323600-226331000	Weak transcription	Fetal Brain Female	brain
39	chr1:226323600-226331200	Weak transcription	Fetal Intestine Small	intestine
40	chr1:226323600-226331200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:226323600-226331600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:226323600-226331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:226323600-226331800	Weak transcription	Liver	Liver
44	chr1:226323600-226333800	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:226323600-226333800	Weak transcription	Esophagus	oesophagus
46	chr1:226323600-226334000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:226323600-226338400	Weak transcription	Fetal Kidney	kidney
48	chr1:226323600-226339800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:226323600-226339800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:226323600-226346000	Weak transcription	Fetal Heart	heart

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