Variant report

Variant	rs4354539
Chromosome Location	chr1:151429083-151429084
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151421812..151434588-chr1:151506621..151515599,30	MCF-7	breast:
2	chr1:151411841..151424302-chr1:151427210..151433048,24	MCF-7	breast:
3	chr1:151427202..151436068-chr1:151477865..151490153,60	MCF-7	breast:
4	chr1:151428938..151433041-chr1:151480813..151490135,53	MCF-7	breast:
5	chr1:151428567..151432402-chr1:151505978..151509700,4	MCF-7	breast:
6	chr1:151371526..151374105-chr1:151428160..151432357,4	K562	blood:
7	chr1:151411812..151418574-chr1:151428106..151433466,11	MCF-7	breast:
8	chr1:151428600..151431654-chr1:151540611..151542217,3	MCF-7	breast:
9	chr1:151428333..151430220-chr1:151430244..151432504,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143375	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000159377	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11204806	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204820	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196346	1.00[CEU][hapmap]
rs1196348	1.00[CEU][hapmap]
rs1196349	1.00[CEU][hapmap]
rs1196351	1.00[CEU][hapmap]
rs1196356	1.00[CEU][hapmap]
rs1196463	1.00[CEU][hapmap]
rs12566457	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566673	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1539493	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs1571294	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16833248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16833263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1781432	1.00[CEU][hapmap]
rs2296840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2997072	1.00[CEU][hapmap]
rs3748549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3818561	1.00[CEU][hapmap]
rs4147451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970916	0.82[EUR][1000 genomes]
rs4970953	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971045	0.83[AMR][1000 genomes]
rs56317453	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58057716	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59153459	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59848815	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587574	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6587586	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6669679	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67750241	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72633634	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72633635	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72633636	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633637	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633638	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633639	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7548614	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9729256	0.91[AMR][1000 genomes];0.82[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv1811070	chr1:151403570-151433317	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4354539	PSMB4	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151398400-151429600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:151401000-151430000	Weak transcription	Esophagus	oesophagus
3	chr1:151401600-151429200	Weak transcription	Spleen	Spleen
4	chr1:151410200-151429800	Weak transcription	Lung	lung
5	chr1:151411400-151430000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:151412600-151429200	Weak transcription	Brain Germinal Matrix	brain
7	chr1:151413600-151429800	Weak transcription	Pancreas	Pancrea
8	chr1:151413600-151430000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:151413800-151429400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:151413800-151429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:151414000-151429600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:151414200-151430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:151414400-151429400	Weak transcription	Fetal Kidney	kidney
14	chr1:151414400-151429400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:151414600-151429200	Weak transcription	Fetal Brain Male	brain
16	chr1:151414600-151430400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:151414800-151429600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:151415000-151429400	Weak transcription	Placenta	Placenta
19	chr1:151416400-151429400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:151416800-151429600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:151417000-151429200	Weak transcription	HUVEC	blood vessel
22	chr1:151417400-151429600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:151418000-151429200	Weak transcription	Left Ventricle	heart
24	chr1:151418400-151429400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:151418400-151429400	Weak transcription	Fetal Heart	heart
26	chr1:151418400-151429600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:151418400-151429600	Weak transcription	Osteobl	bone
28	chr1:151418600-151429200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:151418600-151429200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:151418600-151429400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:151418600-151429400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:151418600-151429600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:151419000-151429400	Weak transcription	Liver	Liver
34	chr1:151421800-151429400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:151421800-151429600	Weak transcription	HMEC	breast
36	chr1:151422000-151429200	Weak transcription	Thymus	Thymus
37	chr1:151422000-151429400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:151422000-151429400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr1:151422000-151430000	Weak transcription	Ovary	ovary
40	chr1:151422400-151429200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:151423200-151429200	Weak transcription	Fetal Intestine Large	intestine
42	chr1:151423200-151429400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:151423200-151429600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:151424800-151429400	Weak transcription	Fetal Thymus	thymus
45	chr1:151425400-151429200	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:151425600-151429600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:151425800-151429200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:151425800-151429400	Weak transcription	Fetal Intestine Small	intestine
49	chr1:151425800-151429800	Weak transcription	Fetal Stomach	stomach
50	chr1:151426800-151429400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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