Variant report

Variant	rs28439002
Chromosome Location	chr2:54018832-54018833
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54016706..54018881-chr2:54023439..54026014,2	K562	blood:
2	chr2:54012419..54016440-chr2:54016510..54019549,4	K562	blood:
3	chr2:54018818..54021003-chr2:54021378..54023244,2	K562	blood:

Variant related genes	Relation type
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10181752	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10181876	0.95[ASN][1000 genomes]
rs10185375	0.88[ASN][1000 genomes]
rs10187718	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10190578	0.89[ASN][1000 genomes]
rs10191950	0.90[ASN][1000 genomes]
rs10193711	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197062	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10200897	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10210726	0.85[ASN][1000 genomes]
rs10211188	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10211650	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10490470	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11684574	0.87[ASN][1000 genomes]
rs12612589	0.93[ASN][1000 genomes]
rs12613682	0.86[ASN][1000 genomes]
rs12616124	0.90[ASN][1000 genomes]
rs12616774	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12617360	0.86[ASN][1000 genomes]
rs12617668	0.92[ASN][1000 genomes]
rs12618587	0.87[ASN][1000 genomes]
rs12620190	0.95[ASN][1000 genomes]
rs12620208	0.95[ASN][1000 genomes]
rs12620325	0.92[ASN][1000 genomes]
rs12621547	0.84[ASN][1000 genomes]
rs12621557	0.87[ASN][1000 genomes]
rs12621635	0.87[ASN][1000 genomes]
rs13383167	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13393197	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13414183	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13414472	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13415842	0.82[ASN][1000 genomes]
rs13421512	0.86[ASN][1000 genomes]
rs13423576	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17045125	0.85[ASN][1000 genomes]
rs17045215	0.90[ASN][1000 genomes]
rs17045292	0.84[ASN][1000 genomes]
rs2009149	0.85[ASN][1000 genomes]
rs2272250	0.82[ASN][1000 genomes]
rs2287344	0.95[ASN][1000 genomes]
rs2287345	0.95[ASN][1000 genomes]
rs28391754	0.86[AFR][1000 genomes]
rs3755120	0.85[ASN][1000 genomes]
rs3770398	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3770400	0.93[ASN][1000 genomes]
rs3770401	0.85[ASN][1000 genomes]
rs3821080	0.91[ASN][1000 genomes]
rs3850345	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3861570	0.92[ASN][1000 genomes]
rs55839073	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545367	0.82[AFR][1000 genomes]
rs6705484	0.90[ASN][1000 genomes]
rs6712204	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6714424	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6717642	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6759437	0.81[AFR][1000 genomes]
rs72793658	0.81[ASN][1000 genomes]
rs7568771	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582542	0.92[ASN][1000 genomes]
rs7586686	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7595713	0.86[ASN][1000 genomes]
rs7595816	0.87[ASN][1000 genomes]
rs7609067	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28439002	ASB3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54024000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54015200-54025400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:54015200-54029800	Weak transcription	Esophagus	oesophagus
4	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
5	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
7	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
8	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:54015400-54021600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:54015600-54020000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:54015600-54021600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:54015600-54022000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:54015600-54022200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:54015600-54022200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:54015600-54022200	Weak transcription	Brain Germinal Matrix	brain
16	chr2:54015600-54022200	Weak transcription	Fetal Kidney	kidney
17	chr2:54015600-54022800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:54015600-54029600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:54015800-54019400	Weak transcription	Fetal Lung	lung
23	chr2:54015800-54019400	Weak transcription	Fetal Stomach	stomach
24	chr2:54015800-54019400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:54015800-54019600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:54015800-54019600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:54015800-54019600	Weak transcription	NHLF	lung
28	chr2:54015800-54019800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:54015800-54019800	Weak transcription	Colonic Mucosa	Colon
30	chr2:54015800-54021000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:54015800-54021000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:54015800-54021000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:54015800-54021000	Weak transcription	HSMM	muscle
34	chr2:54015800-54021000	Weak transcription	NHDF-Ad	bronchial
35	chr2:54015800-54021200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:54015800-54021200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr2:54015800-54021200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:54015800-54021200	Weak transcription	Placenta	Placenta
39	chr2:54015800-54021400	Weak transcription	Fetal Thymus	thymus
40	chr2:54015800-54021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:54015800-54022000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:54015800-54022000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:54015800-54022000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:54015800-54022000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:54015800-54022000	Weak transcription	Adipose Nuclei	Adipose
46	chr2:54015800-54022000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:54015800-54022000	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:54015800-54022000	Weak transcription	NH-A	brain
49	chr2:54015800-54022200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:54015800-54022200	Weak transcription	Primary T cells from cord blood	blood

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