Variant report

Variant	rs10007409
Chromosome Location	chr4:120142306-120142307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120133051..120135487-chr4:120141278..120144342,3	MCF-7	breast:
2	chr4:120138762..120140367-chr4:120140533..120142369,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP53-1	chr4:120138705-120142650	NONHSAT098036

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11737086	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1397610	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4374607	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56153161	0.81[ASN][1000 genomes]
rs56894567	0.81[ASN][1000 genomes]
rs67110248	0.81[ASN][1000 genomes]
rs6833072	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72673792	0.81[ASN][1000 genomes]
rs7440443	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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
rs10007409	USP53	Cis_1M	lymphoblastoid	RTeQTL
rs10007409	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs10007409	RP11-33B1.1	cis	Nerve Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134600-120144600	Weak transcription	Spleen	Spleen
2	chr4:120134800-120143400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:120134800-120147000	Weak transcription	Fetal Brain Male	brain
4	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:120135000-120142600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:120135000-120142800	Weak transcription	Lung	lung
7	chr4:120135000-120154800	Weak transcription	Primary B cells from cord blood	blood
8	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:120135200-120143200	Weak transcription	Brain Substantia Nigra	brain
11	chr4:120135200-120143600	Weak transcription	Thymus	Thymus
12	chr4:120135200-120155000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:120135200-120155000	Weak transcription	Small Intestine	intestine
14	chr4:120135200-120163600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:120135400-120142400	Weak transcription	Fetal Intestine Small	intestine
18	chr4:120135400-120159000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:120135600-120142800	Weak transcription	Fetal Stomach	stomach
21	chr4:120135600-120155000	Weak transcription	K562	blood
22	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
23	chr4:120136000-120145600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:120136200-120143000	Weak transcription	NH-A	brain
25	chr4:120136200-120147400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:120136200-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:120136200-120154400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
29	chr4:120136400-120151600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:120136400-120155000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:120136400-120155000	Weak transcription	Stomach Mucosa	stomach
32	chr4:120136400-120156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:120136600-120142800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:120137000-120151000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:120137400-120155000	Weak transcription	Right Atrium	heart
36	chr4:120137600-120154600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:120138400-120144400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:120138400-120144600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:120138400-120144800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:120138600-120143800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:120138600-120148000	Weak transcription	Pancreas	Pancrea
42	chr4:120138800-120155000	Weak transcription	Fetal Thymus	thymus
43	chr4:120139000-120148400	Weak transcription	Gastric	stomach
44	chr4:120139400-120143400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:120139400-120143800	Strong transcription	HSMM	muscle
46	chr4:120139400-120149200	Weak transcription	Fetal Heart	heart
47	chr4:120139400-120151400	Weak transcription	HepG2	liver
48	chr4:120139400-120151600	Weak transcription	Psoas Muscle	Psoas
49	chr4:120139400-120165800	Weak transcription	Fetal Kidney	kidney
50	chr4:120139600-120142400	Weak transcription	Placenta	Placenta

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