Variant report

Variant	rs4819138
Chromosome Location	chr21:47061267-47061268
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	STAT3	chr21:47061101-47061301	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr21:47061049-47061390	GM12878	blood:	n/a	n/a
3	CTCF	chr21:47061120-47061270	BE2_C	brain:	n/a	n/a
4	PAX5	chr21:47060930-47061306	GM12878	blood:	n/a	chr21:47061057-47061075
5	POU2F2	chr21:47060926-47061391	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:47060875-47061418	GM12878	blood:	n/a	n/a
7	EP300	chr21:47060351-47061457	GM12878	blood:	n/a	chr21:47060415-47060431
8	RAD21	chr21:47061002-47061285	H1-hESC	embryonic stem cell:	n/a	chr21:47061120-47061134 chr21:47061083-47061092
9	CHD1	chr21:47061045-47061484	GM12878	blood:	n/a	n/a
10	EBF1	chr21:47061018-47061441	GM12878	blood:	n/a	n/a
11	POLR2A	chr21:47060875-47061491	GM12878	blood:	n/a	n/a
12	SMC3	chr21:47061030-47061368	GM12878	blood:	n/a	n/a
13	CTCF	chr21:47060877-47061283	H1-hESC	embryonic stem cell:	n/a	n/a
14	ZNF384	chr21:47061054-47061564	GM12878	blood:	n/a	n/a
15	RAD21	chr21:47061018-47061274	HepG2	liver:	n/a	chr21:47061120-47061134 chr21:47061083-47061092
16	CTCF	chr21:47061120-47061270	GM12864	blood:	n/a	n/a
17	POLR2A	chr21:47060907-47061402	GM12878	blood:	n/a	n/a
18	STAT3	chr21:47061101-47061268	MCF10A-Er-Src	breast:	n/a	n/a
19	CHD2	chr21:47061034-47061432	GM12878	blood:	n/a	n/a
20	MXI1	chr21:47060869-47061369	GM12878	blood:	n/a	n/a
21	CTCF	chr21:47061140-47061290	GM12864	blood:	n/a	n/a
22	MAX	chr21:47060962-47061369	GM12878	blood:	n/a	n/a
23	EBF1	chr21:47060971-47061404	GM12878	blood:	n/a	n/a
24	MXI1	chr21:47058565-47061304	SK-N-SH	brain:	n/a	n/a
25	WRNIP1	chr21:47061225-47061272	GM12878	blood:	n/a	n/a
26	CTCF	chr21:47061160-47061310	GM12864	blood:	n/a	n/a
27	CTCF	chr21:47061120-47061270	NHDF-neo	bronchial:	n/a	n/a
28	CTCF	chr21:47060959-47061343	GM12878	blood:	n/a	n/a
29	BATF	chr21:47061123-47061436	GM12878	blood:	n/a	n/a
30	CTCF	chr21:47061160-47061310	HFF-Myc	foreskin:	n/a	n/a
31	BHLHE40	chr21:47061076-47061349	GM12878	blood:	n/a	chr21:47061125-47061141
32	MAX	chr21:47060762-47061392	MCF-7	breast:	n/a	n/a
33	TBP	chr21:47060988-47061436	GM12878	blood:	n/a	n/a
34	PAX5	chr21:47061040-47061402	GM12878	blood:	n/a	chr21:47061057-47061075
35	CTCF	chr21:47060987-47061289	K562	blood:	n/a	n/a
36	ZNF143	chr21:47061009-47061364	GM12878	blood:	n/a	n/a
37	RAD21	chr21:47060880-47061359	H1-hESC	embryonic stem cell:	n/a	chr21:47061120-47061134 chr21:47061083-47061092
38	MAZ	chr21:47060968-47061493	GM12878	blood:	n/a	n/a
39	POLR2A	chr21:47060951-47061291	GM12878	blood:	n/a	n/a
40	BATF	chr21:47061144-47061475	GM12878	blood:	n/a	n/a
41	SP1	chr21:47060954-47061333	GM12878	blood:	n/a	chr21:47061200-47061209 chr21:47061137-47061146 chr21:47061135-47061147 chr21:47061137-47061146 chr21:47061198-47061210 chr21:47061198-47061210 chr21:47061136-47061145 chr21:47061135-47061147 chr21:47061136-47061146 chr21:47061195-47061209

No.	Distal block	Cell Line	Cell type
1	chr21:47054503..47058217-chr21:47058461..47061717,3	K562	blood:
2	chr21:46961035..46963239-chr21:47061163..47064234,4	MCF-7	breast:
3	chr21:47058472..47062802-chr21:47073375..47076804,3	MCF-7	breast:
4	chr21:47035998..47037896-chr21:47060266..47063425,3	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	chr21:47012314..47016239-chr21:47061189..47064828,5	K562	blood:

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

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11908836	0.86[CHB][hapmap]
rs11911348	0.80[CHB][hapmap]
rs12152003	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2838970	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838971	0.95[ASN][1000 genomes]
rs2838975	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2838977	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2839008	0.83[CHD][hapmap]
rs2877078	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3945438	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819133	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819137	0.96[ASN][1000 genomes]
rs4819142	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322208	0.82[ASN][1000 genomes]
rs725930	0.80[CHB][hapmap]
rs7276178	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7278258	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs7280089	0.80[CHB][hapmap]
rs7282214	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736063	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7410098	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7509868	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs767138	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128681	0.96[ASN][1000 genomes]
rs8130662	0.81[EUR][1000 genomes]
rs8133338	0.80[CHB][hapmap]
rs9653790	0.96[ASN][1000 genomes]
rs9798668	0.90[CHB][hapmap]
rs9977594	0.80[CHB][hapmap]
rs9977706	0.96[ASN][1000 genomes]
rs9978583	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4819138	PCBP3	cis	Artery Tibial	GTEx
rs4819138	TFF1	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47056400-47063600	Weak transcription	K562	blood
2	chr21:47056600-47061400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:47056600-47063600	Weak transcription	Pancreas	Pancrea
4	chr21:47056800-47061400	Enhancers	Thymus	Thymus
5	chr21:47057200-47061400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:47058000-47061400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr21:47058800-47061800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:47058800-47062000	Enhancers	Primary B cells from peripheral blood	blood
9	chr21:47058800-47062200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr21:47059000-47062000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr21:47059200-47062000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr21:47059200-47062200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:47059400-47062000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr21:47059400-47062400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr21:47059400-47062400	Enhancers	Spleen	Spleen
16	chr21:47059600-47061400	Enhancers	Duodenum Mucosa	Duodenum
17	chr21:47059600-47061400	Enhancers	Fetal Thymus	thymus
18	chr21:47059800-47061600	Enhancers	Colonic Mucosa	Colon
19	chr21:47059800-47061800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:47059800-47062000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr21:47059800-47062400	Enhancers	Primary B cells from cord blood	blood
22	chr21:47060200-47061600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr21:47060200-47061600	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr21:47060200-47061800	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr21:47060200-47062000	Bivalent Enhancer	Placenta	Placenta
26	chr21:47060200-47062200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr21:47060200-47062400	Bivalent Enhancer	Brain Germinal Matrix	brain
28	chr21:47060400-47061400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr21:47060400-47061800	Enhancers	NHEK	skin
30	chr21:47060400-47062200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr21:47060400-47062400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr21:47060600-47061400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr21:47060600-47061600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr21:47060600-47061600	Weak transcription	Gastric	stomach
35	chr21:47060600-47061600	Weak transcription	Lung	lung
36	chr21:47060600-47061800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:47060600-47062000	Weak transcription	Dnd41	blood
38	chr21:47060600-47062200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr21:47060600-47062400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr21:47060600-47062800	Enhancers	Primary T cells from cord blood	blood
41	chr21:47060800-47061600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr21:47060800-47061600	Weak transcription	Small Intestine	intestine
43	chr21:47060800-47061600	Enhancers	NHDF-Ad	bronchial
44	chr21:47060800-47062000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
45	chr21:47060800-47062000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr21:47060800-47063600	Weak transcription	HSMMtube	muscle
47	chr21:47060800-47064200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr21:47061000-47061400	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr21:47061000-47061400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr21:47061000-47061400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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