Variant report

Variant	rs56122576
Chromosome Location	chr4:120129336-120129337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr4:120129331-120129538	HepG2	liver:	n/a	chr4:120129448-120129459 chr4:120129449-120129460 chr4:120129449-120129460 chr4:120129444-120129460 chr4:120129447-120129461

No.	Distal block	Cell Line	Cell type
1	chr4:120125197..120131905-chr4:120131994..120135569,17	K562	blood:
2	chr4:120100153..120102490-chr4:120128940..120130617,2	MCF-7	breast:
3	chr4:120060171..120063563-chr4:120128883..120130877,3	MCF-7	breast:

Variant related genes	Relation type
USP53	TF binding region
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10006304	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010696	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10013032	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10022262	0.82[AMR][1000 genomes]
rs10022508	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029750	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10031033	0.85[EUR][1000 genomes]
rs1011054	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10213342	0.83[EUR][1000 genomes]
rs1033087	0.91[ASN][1000 genomes]
rs11098490	0.87[ASN][1000 genomes]
rs11098491	0.87[ASN][1000 genomes]
rs11098492	0.90[ASN][1000 genomes]
rs11098493	0.90[ASN][1000 genomes]
rs11098496	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11098499	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11726229	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11729897	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11733239	0.86[ASN][1000 genomes]
rs11734519	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11931312	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11944880	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12186259	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12499598	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12501610	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12502503	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12506395	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12509054	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512517	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12513191	0.90[ASN][1000 genomes]
rs13113112	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13114751	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13116504	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13120560	0.88[ASN][1000 genomes]
rs13123591	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13126596	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13129661	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13133044	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13136593	0.90[ASN][1000 genomes]
rs13138782	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13435802	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1397608	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1511015	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1511018	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1511019	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1551	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17839089	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036861	0.91[ASN][1000 genomes]
rs2203039	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28374891	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28419773	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28452522	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28555550	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34585914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34616304	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34630083	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35197422	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35271032	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35434465	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35643470	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35916640	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3749591	0.87[AMR][1000 genomes]
rs4145951	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4355373	0.87[ASN][1000 genomes]
rs4833612	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833613	0.86[ASN][1000 genomes]
rs56386062	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6534130	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67073020	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68128210	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6814412	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6815725	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6822498	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6826823	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832670	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6837898	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6838674	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6845702	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6849889	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6851130	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6851169	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7441137	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7659194	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7661020	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7684942	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7685268	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs951570	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9884728	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9993110	0.88[ASN][1000 genomes]
rs9995277	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996382	0.84[EUR][1000 genomes];0.97[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs56122576	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs56122576	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs56122576	RP11-33B1.1	cis	Whole Blood	GTEx
rs56122576	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs56122576	RP11-384K6.6	cis	Artery Tibial	GTEx
rs56122576	RP11-33B1.1	cis	lung	GTEx
rs56122576	RP11-384K6.6	cis	Whole Blood	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120101000-120132400	Weak transcription	Left Ventricle	heart
2	chr4:120117600-120133200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120119600-120129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:120125600-120129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:120125600-120131400	Enhancers	HSMMtube	muscle
6	chr4:120125800-120131800	Enhancers	HSMM	muscle
7	chr4:120125800-120132200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:120126000-120129400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:120126200-120131200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:120126200-120132200	Enhancers	NHDF-Ad	bronchial
11	chr4:120126400-120129400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:120126400-120129400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:120126400-120129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:120126400-120130800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:120126400-120132200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:120126400-120132400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:120126400-120132400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:120126400-120132400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:120126400-120132400	Enhancers	HUVEC	blood vessel
20	chr4:120126400-120132600	Weak transcription	Right Atrium	heart
21	chr4:120127200-120129800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:120127400-120132200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:120127400-120132400	Enhancers	NHLF	lung
24	chr4:120127600-120130200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:120128000-120132800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:120128400-120130000	Enhancers	A549	lung
27	chr4:120128400-120132400	Weak transcription	Adipose Nuclei	Adipose
28	chr4:120128600-120129600	Weak transcription	HMEC	breast
29	chr4:120128600-120129600	Weak transcription	K562	blood
30	chr4:120128600-120129600	Weak transcription	NHEK	skin
31	chr4:120128600-120129800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:120128600-120129800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:120128600-120129800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:120128600-120130000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:120128600-120130200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:120128600-120130200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:120128600-120130600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:120128600-120130800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:120128600-120132400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:120128600-120132400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr4:120128600-120132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:120128800-120129800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:120128800-120130400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:120129000-120130000	Weak transcription	Osteobl	bone
45	chr4:120129000-120132800	Weak transcription	Fetal Heart	heart
46	chr4:120129200-120129600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:120129200-120130800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr4:120129200-120132400	Weak transcription	Fetal Lung	lung

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