Variant report

Variant	rs4900572
Chromosome Location	chr14:103868851-103868852
allele	C/T
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	CEBPB	chr14:103868680-103868963	K562	blood:	n/a	chr14:103868839-103868850
2	CEBPB	chr14:103868736-103868884	A549	lung:	n/a	chr14:103868839-103868850
3	CEBPB	chr14:103868736-103869027	K562	blood:	n/a	chr14:103868839-103868850
4	CEBPB	chr14:103868731-103869400	Hela-S3	cervix:	n/a	chr14:103868839-103868850
5	CEBPB	chr14:103868716-103869028	H1-hESC	embryonic stem cell:	n/a	chr14:103868839-103868850
6	CEBPB	chr14:103868765-103868907	HepG2	liver:	n/a	chr14:103868839-103868850

No.	Distal block	Cell Line	Cell type
1	chr14:103868073..103870458-chr14:103882409..103885335,2	MCF-7	breast:
2	chr14:103798722..103803234-chr14:103866449..103871829,6	MCF-7	breast:
3	chr14:103858689..103864179-chr14:103864270..103870415,8	K562	blood:
4	chr14:103867682..103870650-chr14:103878470..103880525,2	K562	blood:
5	chr14:103866682..103869641-chr14:103890743..103893905,3	MCF-7	breast:
6	chr14:103798810..103800403-chr14:103867650..103869868,2	K562	blood:

Variant related genes	Relation type
MARK3	TF binding region
ENSG00000100664	Chromatin interaction
ENSG00000244691	Chromatin interaction
ENSG00000075413	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10133035	0.80[EUR][1000 genomes]
rs10134580	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1013650	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10139279	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10141120	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10141388	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10141433	0.86[EUR][1000 genomes]
rs10143247	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10145793	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10150072	0.83[EUR][1000 genomes]
rs1028613	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621510	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11622356	0.81[EUR][1000 genomes]
rs11623869	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11624367	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11626483	0.84[EUR][1000 genomes]
rs11628213	0.87[EUR][1000 genomes]
rs11628969	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12879085	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12888077	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12889639	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12890750	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12898029	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17617941	0.87[EUR][1000 genomes]
rs17679475	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1951392	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961600	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1989565	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2010281	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273699	0.81[AMR][1000 genomes]
rs2273700	0.88[EUR][1000 genomes]
rs2273703	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2403180	0.89[EUR][1000 genomes]
rs28369539	0.87[EUR][1000 genomes]
rs28444993	0.88[EUR][1000 genomes]
rs28496120	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28583452	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28626081	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34216351	0.88[EUR][1000 genomes]
rs3742458	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3783394	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3783395	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783402	0.84[EUR][1000 genomes]
rs3825566	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906321	0.85[EUR][1000 genomes]
rs55859054	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56365443	0.87[EUR][1000 genomes]
rs62006268	0.87[EUR][1000 genomes]
rs62007681	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62007683	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62007684	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62007686	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62007687	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62007718	0.89[EUR][1000 genomes]
rs62007719	0.89[EUR][1000 genomes]
rs6575983	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6575984	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140564	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145113	0.89[EUR][1000 genomes]
rs7146506	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7150317	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7152202	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7154246	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7155014	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7156150	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7156619	0.81[AMR][1000 genomes]
rs7158144	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7158822	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7160208	0.85[EUR][1000 genomes]
rs7160366	0.89[EUR][1000 genomes]
rs72708854	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72708874	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72708893	0.88[EUR][1000 genomes]
rs8013101	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8015918	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8019578	0.83[EUR][1000 genomes]
rs9671911	0.84[EUR][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	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4900572	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs4900572	MARK3	cis	Thyroid	GTEx
rs4900572	CKB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103855000-103874800	Weak transcription	Fetal Brain Male	brain
2	chr14:103855200-103871800	Weak transcription	Brain Germinal Matrix	brain
3	chr14:103856600-103871200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr14:103856600-103871600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:103857000-103871000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr14:103858800-103871400	Weak transcription	Fetal Brain Female	brain
7	chr14:103860400-103871400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr14:103860800-103871400	Weak transcription	Fetal Intestine Large	intestine
9	chr14:103861000-103874800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:103861000-103882400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:103862000-103919400	Weak transcription	Colonic Mucosa	Colon
12	chr14:103862400-103870200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr14:103863200-103870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:103863800-103871600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr14:103864200-103871200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr14:103864200-103871400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr14:103864400-103869200	Enhancers	Psoas Muscle	Psoas
18	chr14:103864400-103870800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr14:103865000-103871400	Weak transcription	Fetal Intestine Small	intestine
20	chr14:103865000-103872200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:103865400-103869600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr14:103865600-103869200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr14:103866000-103869200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr14:103866000-103869200	Enhancers	Adipose Nuclei	Adipose
25	chr14:103866000-103870800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr14:103866000-103870800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr14:103866000-103871200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr14:103866200-103869200	Enhancers	Right Ventricle	heart
29	chr14:103866400-103869800	Enhancers	Thymus	Thymus
30	chr14:103866400-103871200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr14:103866400-103871400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr14:103866400-103871400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr14:103866400-103871600	Enhancers	Brain Anterior Caudate	brain
34	chr14:103866600-103869200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr14:103866600-103869200	Enhancers	Colon Smooth Muscle	Colon
36	chr14:103866600-103869800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:103866600-103870200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr14:103866600-103870600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr14:103866600-103870600	Weak transcription	Lung	lung
40	chr14:103866600-103871000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:103866600-103883400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr14:103866800-103869200	Enhancers	HUVEC	blood vessel
43	chr14:103866800-103869400	Enhancers	Small Intestine	intestine
44	chr14:103866800-103870000	Enhancers	Primary B cells from cord blood	blood
45	chr14:103866800-103870400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr14:103866800-103870600	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr14:103866800-103871600	Enhancers	Brain Angular Gyrus	brain
48	chr14:103866800-103871600	Enhancers	Brain Hippocampus Middle	brain
49	chr14:103867000-103869200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr14:103867000-103870800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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