Variant report

Variant	rs34478210
Chromosome Location	chr4:120135901-120135902
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	chr4:120132453..120136158-chr4:120220202..120223113,6	K562	blood:
2	chr4:120133904..120136281-chr4:120160209..120162488,2	K562	blood:
3	chr4:120132319..120136069-chr4:120219720..120222326,6	MCF-7	breast:
4	chr4:119929578..119931814-chr4:120134367..120136191,2	MCF-7	breast:
5	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
6	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
7	chr4:120135683..120139128-chr4:120180501..120183210,3	K562	blood:
8	chr4:120135683..120138360-chr4:120179744..120182686,3	K562	blood:
9	chr1:109939637..109942305-chr4:120134026..120136766,2	MCF-7	breast:
10	chr4:119959493..119961509-chr4:120134410..120137217,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164109	Chromatin interaction
ENSG00000145390	Chromatin interaction
ENSG00000164096	Chromatin interaction
ENSG00000134243	Chromatin interaction
ENSG00000250938	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11725433	0.90[ASN][1000 genomes]
rs11729857	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11733606	0.90[ASN][1000 genomes]
rs11737560	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104050	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13106878	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113462	0.90[ASN][1000 genomes]
rs13113662	0.90[ASN][1000 genomes]
rs13127517	0.81[ASN][1000 genomes]
rs13140255	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13144426	0.90[ASN][1000 genomes]
rs1511021	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511022	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334151	0.90[ASN][1000 genomes]
rs17517075	0.85[ASN][1000 genomes]
rs34156358	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34624042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951506	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35137697	0.90[ASN][1000 genomes]
rs35612705	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35646004	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35830965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62328380	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62328402	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62328403	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62328404	0.90[ASN][1000 genomes]
rs6846936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610255	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655064	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7678138	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34478210	RP11-33B1.1	cis	Thyroid	GTEx
rs34478210	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs34478210	USP53	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120132000-120137000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:120132200-120136400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr4:120132400-120136200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:120132400-120136200	Active TSS	NH-A	brain
5	chr4:120132400-120136400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:120132400-120136400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:120132400-120136400	Active TSS	Stomach Smooth Muscle	stomach
8	chr4:120132400-120137000	Active TSS	Right Ventricle	heart
9	chr4:120132600-120136000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr4:120132600-120136000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:120132600-120136000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:120132600-120136000	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr4:120132600-120136000	Active TSS	Osteobl	bone
14	chr4:120132600-120136200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr4:120132600-120136200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:120132600-120136200	Active TSS	HMEC	breast
17	chr4:120132600-120136600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:120132600-120136600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr4:120132600-120136600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:120132600-120136800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:120132600-120136800	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:120132600-120136800	Active TSS	NHEK	skin
23	chr4:120132600-120137000	Active TSS	NHDF-Ad	bronchial
24	chr4:120132600-120137200	Active TSS	NHLF	lung
25	chr4:120132600-120137400	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr4:120132600-120138200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:120132800-120136200	Active TSS	HSMMtube	muscle
28	chr4:120132800-120136400	Active TSS	Brain Hippocampus Middle	brain
29	chr4:120132800-120136400	Active TSS	Colonic Mucosa	Colon
30	chr4:120132800-120136400	Active TSS	Hela-S3	cervix
31	chr4:120132800-120136600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:120133000-120136200	Active TSS	Brain Angular Gyrus	brain
33	chr4:120133000-120136200	Active TSS	HSMM	muscle
34	chr4:120133000-120136400	Active TSS	Aorta	Aorta
35	chr4:120133200-120136000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr4:120133200-120136200	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr4:120134200-120136000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:120134400-120137200	Active TSS	Right Atrium	heart
39	chr4:120134400-120137600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:120134600-120144600	Weak transcription	Spleen	Spleen
41	chr4:120134800-120136400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:120134800-120138800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:120134800-120142000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:120134800-120143400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:120134800-120147000	Weak transcription	Fetal Brain Male	brain
46	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:120135000-120136200	Enhancers	Primary T cells from cord blood	blood
48	chr4:120135000-120136200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr4:120135000-120136400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr4:120135000-120137000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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