Variant report

Variant	rs12152003
Chromosome Location	chr21:47062707-47062708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:47062622-47062883	MCF-7	breast:	n/a	n/a
2	MAZ	chr21:47062447-47063794	GM12878	blood:	n/a	chr21:47062467-47062477
3	MYC	chr21:47062694-47062708	MCF-7	breast:	n/a	n/a
4	POLR2A	chr21:47062197-47063005	MCF-7	breast:	n/a	n/a
5	BACH1	chr21:47062063-47063101	H1-hESC	embryonic stem cell:	n/a	n/a
6	BHLHE40	chr21:47062639-47062859	GM12878	blood:	n/a	n/a
7	GABPA	chr21:47062639-47062871	H1-hESC	embryonic stem cell:	n/a	chr21:47062664-47062673
8	MAZ	chr21:47062346-47064616	IMR90	lung:	n/a	chr21:47064383-47064390 chr21:47062467-47062477
9	POLR2A	chr21:47062215-47062938	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46961035..46963239-chr21:47061163..47064234,4	MCF-7	breast:
2	chr21:47058472..47062802-chr21:47073375..47076804,3	MCF-7	breast:
3	chr21:47035998..47037896-chr21:47060266..47063425,3	MCF-7	breast:
4	chr21:46963704..46966676-chr21:47062691..47065405,2	MCF-7	breast:
5	chr21:47060499..47063225-chr21:47086755..47088271,2	MCF-7	breast:
6	chr21:47039810..47042625-chr21:47060618..47063331,3	MCF-7	breast:
7	chr21:47061104..47062756-chr21:47743383..47745371,2	MCF-7	breast:
8	chr21:47061926..47064777-chr21:47168199..47170677,2	MCF-7	breast:
9	chr21:47012314..47016239-chr21:47061189..47064828,5	K562	blood:

No data

Variant related genes	Relation type
PCBP3	TF binding region
ENSG00000160298	Chromatin interaction
ENSG00000183570	Chromatin interaction
ENSG00000173638	Chromatin interaction
ENSG00000233922	Chromatin interaction
ENSG00000160299	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2838975	0.81[EUR][1000 genomes]
rs2877078	0.82[EUR][1000 genomes]
rs4819138	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7276178	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7282214	0.82[EUR][1000 genomes]
rs736063	0.81[EUR][1000 genomes]
rs7410098	0.82[EUR][1000 genomes]
rs7509868	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2762114	chr21:46680202-47067744	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
5	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
6	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
7	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
8	nsv914077	chr21:46998548-47091361	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
10	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
11	nsv587864	chr21:47053453-47070718	Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
12	esv3338089	chr21:47061324-47064672	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv3448839	chr21:47061324-47065322	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	esv3376015	chr21:47061349-47064897	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
15	esv3326927	chr21:47061524-47065022	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12152003	PCBP3	cis	Muscle Skeletal	GTEx
rs12152003	PCBP3	cis	Artery Tibial	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47056400-47063600	Weak transcription	K562	blood
2	chr21:47056600-47063600	Weak transcription	Pancreas	Pancrea
3	chr21:47060600-47062800	Enhancers	Primary T cells from cord blood	blood
4	chr21:47060800-47063600	Weak transcription	HSMMtube	muscle
5	chr21:47060800-47064200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr21:47061200-47064200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr21:47061400-47062800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr21:47061400-47062800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr21:47061400-47063600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr21:47061600-47063600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr21:47061600-47064000	Weak transcription	NHDF-Ad	bronchial
12	chr21:47061600-47064200	Active TSS	Thymus	Thymus
13	chr21:47061800-47062800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr21:47061800-47063600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:47061800-47063800	Weak transcription	NHEK	skin
16	chr21:47061800-47064000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr21:47062000-47062800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr21:47062000-47062800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr21:47062000-47062800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr21:47062000-47064000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr21:47062000-47064200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr21:47062200-47062800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:47062200-47062800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr21:47062200-47062800	Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr21:47062200-47062800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr21:47062200-47062800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr21:47062200-47062800	Active TSS	Adipose Nuclei	Adipose
28	chr21:47062200-47063000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr21:47062200-47063000	Active TSS	Fetal Thymus	thymus
30	chr21:47062200-47063000	Bivalent/Poised TSS	Psoas Muscle	Psoas
31	chr21:47062200-47063600	Weak transcription	Gastric	stomach
32	chr21:47062200-47064600	Active TSS	Colonic Mucosa	Colon
33	chr21:47062400-47062800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:47062400-47062800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr21:47062400-47062800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr21:47062400-47062800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr21:47062400-47062800	Active TSS	Brain Substantia Nigra	brain
38	chr21:47062400-47062800	Active TSS	Lung	lung
39	chr21:47062400-47062800	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr21:47062400-47062800	Active TSS	Rectal Smooth Muscle	rectum
41	chr21:47062400-47062800	Flanking Active TSS	Right Ventricle	heart
42	chr21:47062400-47062800	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr21:47062400-47062800	Active TSS	Stomach Smooth Muscle	stomach
44	chr21:47062400-47062800	Active TSS	HSMM	muscle
45	chr21:47062400-47062800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr21:47062400-47062800	Active TSS	NH-A	brain
47	chr21:47062400-47063000	Enhancers	Primary hematopoietic stem cells	blood
48	chr21:47062400-47063200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
49	chr21:47062400-47064400	Active TSS	Ovary	ovary
50	chr21:47062400-47064400	Active TSS	Right Atrium	heart

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