Variant report

Variant	rs62328404
Chromosome Location	chr4:120207082-120207083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119961537..119963870-chr4:120206398..120209055,3	MCF-7	breast:
2	chr4:120134118..120136397-chr4:120205863..120208720,4	K562	blood:
3	chr4:119963035..119963736-chr4:120207018..120208135,3	MCF-7	breast:
4	chr4:120134118..120136397-chr4:120205863..120208720,2	K562	blood:
5	chr4:120206707..120209312-chr4:120220006..120222573,2	MCF-7	breast:
6	chr4:120200762..120202718-chr4:120206492..120209144,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000164096	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11722431	0.81[EUR][1000 genomes]
rs11722940	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11724619	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11725409	0.81[EUR][1000 genomes]
rs11725433	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728178	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11729960	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11733606	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734624	0.81[EUR][1000 genomes]
rs11734808	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11736997	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11737068	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11737560	0.90[ASN][1000 genomes]
rs13104050	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106878	0.90[ASN][1000 genomes]
rs13112320	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13113462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122306	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13127517	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139711	0.87[EUR][1000 genomes]
rs13140255	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397611	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1511021	0.90[ASN][1000 genomes]
rs1511022	0.90[ASN][1000 genomes]
rs17050312	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17334151	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517075	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17517470	0.81[ASN][1000 genomes]
rs17595468	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17595769	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17595790	0.81[ASN][1000 genomes]
rs2036859	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34125807	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34156358	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478210	0.90[ASN][1000 genomes]
rs34624042	0.90[ASN][1000 genomes]
rs34733524	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34878806	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34951506	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35137697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35225855	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35612705	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646004	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35830965	0.90[ASN][1000 genomes]
rs35846514	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35917388	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817230	0.81[ASN][1000 genomes]
rs3817242	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56818816	0.85[ASN][1000 genomes]
rs62320715	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320716	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320717	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320718	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320719	0.80[ASN][1000 genomes]
rs62320720	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320721	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320722	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320723	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320724	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320725	0.82[EUR][1000 genomes];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]
rs62322274	0.81[EUR][1000 genomes]
rs62322275	0.81[EUR][1000 genomes]
rs62322276	0.83[EUR][1000 genomes]
rs62328380	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328402	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328403	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328408	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328420	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822097	0.92[EUR][1000 genomes]
rs6846936	0.90[ASN][1000 genomes]
rs71610255	0.90[ASN][1000 genomes]
rs71627784	0.97[EUR][1000 genomes]
rs72918504	0.82[EUR][1000 genomes];0.81[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	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
5	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62328404	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs62328404	USP53	cis	Whole Blood	GTEx
rs62328404	RP11-33B1.1	cis	Thyroid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
2	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:120177000-120213600	Weak transcription	Lung	lung
4	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
6	chr4:120177200-120213600	Weak transcription	Esophagus	oesophagus
7	chr4:120177800-120211400	Weak transcription	HepG2	liver
8	chr4:120178200-120213400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:120178200-120213600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:120178200-120213800	Weak transcription	Primary B cells from cord blood	blood
11	chr4:120178600-120217600	Weak transcription	Fetal Stomach	stomach
12	chr4:120187000-120219200	Weak transcription	Right Ventricle	heart
13	chr4:120193000-120217600	Weak transcription	Psoas Muscle	Psoas
14	chr4:120193000-120219200	Weak transcription	Fetal Brain Male	brain
15	chr4:120193200-120212600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:120193800-120213600	Weak transcription	Left Ventricle	heart
17	chr4:120194600-120213400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:120195000-120211800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:120195200-120208200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:120201200-120212400	Weak transcription	Placenta	Placenta
21	chr4:120201200-120220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:120201200-120220200	Weak transcription	Gastric	stomach
23	chr4:120201400-120220200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:120201800-120208800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:120201800-120213600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:120201800-120213800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:120202000-120213400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:120202000-120213600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:120202000-120220200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:120202400-120211800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:120203000-120213600	Weak transcription	Primary T cells from cord blood	blood
32	chr4:120205400-120207200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:120205800-120207600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:120206000-120207200	Genic enhancers	HSMM	muscle
35	chr4:120206200-120208600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:120206400-120207200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:120206400-120211600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:120206400-120213200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:120206400-120213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:120206400-120213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:120206400-120213400	Weak transcription	Ovary	ovary
42	chr4:120206400-120217400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:120206400-120217600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:120206400-120217600	Weak transcription	Fetal Intestine Small	intestine
45	chr4:120206400-120218200	Weak transcription	Aorta	Aorta
46	chr4:120206400-120219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:120206400-120219600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:120206400-120219800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:120206400-120219800	Weak transcription	Brain Substantia Nigra	brain
50	chr4:120206400-120220000	Weak transcription	Colonic Mucosa	Colon

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