Variant report

Variant	rs62328380
Chromosome Location	chr4:120187656-120187657
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120182924..120185910-chr4:120187445..120191655,4	K562	blood:
2	chr4:120132754..120134825-chr4:120185311..120187985,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11722940	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11724619	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11725433	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728178	0.81[ASN][1000 genomes]
rs11729960	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11733606	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734808	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11736997	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11737068	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11737560	0.90[ASN][1000 genomes]
rs13104050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106878	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13112320	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13113462	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113662	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122306	0.81[ASN][1000 genomes]
rs13127517	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139711	0.83[EUR][1000 genomes]
rs13140255	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144426	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397611	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1511021	0.90[ASN][1000 genomes]
rs1511022	0.90[ASN][1000 genomes]
rs17050312	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17334151	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517075	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17517470	0.81[ASN][1000 genomes]
rs17595468	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17595769	0.81[ASN][1000 genomes]
rs17595790	0.81[ASN][1000 genomes]
rs2036859	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34125807	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34156358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478210	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34624042	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34733524	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34878806	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34951506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35137697	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35225855	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35612705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35830965	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35846514	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35917388	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817230	0.81[ASN][1000 genomes]
rs3817242	0.81[ASN][1000 genomes]
rs56818816	0.85[ASN][1000 genomes]
rs62320715	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320716	0.81[ASN][1000 genomes]
rs62320717	0.81[ASN][1000 genomes]
rs62320718	0.81[ASN][1000 genomes]
rs62320719	0.80[ASN][1000 genomes]
rs62320720	0.81[ASN][1000 genomes]
rs62320721	0.81[ASN][1000 genomes]
rs62320722	0.81[ASN][1000 genomes]
rs62320723	0.81[ASN][1000 genomes]
rs62320724	0.81[ASN][1000 genomes]
rs62320725	0.81[ASN][1000 genomes]
rs62320731	0.81[ASN][1000 genomes]
rs62320732	0.81[ASN][1000 genomes]
rs62320733	0.81[ASN][1000 genomes]
rs62320735	0.81[ASN][1000 genomes]
rs62320737	0.81[ASN][1000 genomes]
rs62326356	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62328402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328404	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328408	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328420	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822097	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6846936	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71610255	0.90[ASN][1000 genomes]
rs71627784	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72918504	0.81[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	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	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
4	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
rs62328380	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs62328380	RP11-33B1.1	cis	Thyroid	GTEx
rs62328380	USP53	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
4	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
5	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:120159800-120188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:120166400-120189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:120166400-120206200	Weak transcription	Small Intestine	intestine
15	chr4:120167000-120194400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:120167800-120192400	Weak transcription	Psoas Muscle	Psoas
17	chr4:120170600-120192600	Weak transcription	Fetal Thymus	thymus
18	chr4:120170600-120206200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:120173400-120195200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:120174200-120191800	Weak transcription	Fetal Lung	lung
21	chr4:120174200-120192600	Weak transcription	Brain Anterior Caudate	brain
22	chr4:120174400-120191600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:120174400-120206200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:120175400-120189400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:120175600-120195200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr4:120176800-120192200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:120176800-120193400	Strong transcription	NHDF-Ad	bronchial
28	chr4:120176800-120194400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:120176800-120200800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:120176800-120202600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:120177000-120191600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:120177000-120192600	Weak transcription	Gastric	stomach
33	chr4:120177000-120194800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:120177000-120195000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:120177000-120205600	Weak transcription	Aorta	Aorta
36	chr4:120177000-120206000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr4:120177000-120213600	Weak transcription	Lung	lung
38	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
40	chr4:120177200-120189400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:120177200-120206200	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:120177200-120213600	Weak transcription	Esophagus	oesophagus
43	chr4:120177800-120211400	Weak transcription	HepG2	liver
44	chr4:120178200-120192400	Weak transcription	NH-A	brain
45	chr4:120178200-120213400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr4:120178200-120213600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:120178200-120213800	Weak transcription	Primary B cells from cord blood	blood
48	chr4:120178400-120192600	Weak transcription	Ovary	ovary
49	chr4:120178600-120189600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:120178600-120192400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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