Variant report

Variant	rs56003736
Chromosome Location	chr1:228281257-228281258
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228274933-228281306	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228281047-228281280	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:228280819-228281325	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:228279300-228281328	K562	blood:	n/a	n/a
6	POLR2A	chr1:228281038-228281290	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:228280696-228282036	K562	blood:	n/a	n/a
8	POLR2A	chr1:228281051-228281711	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:228280968-228281395	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:228280841-228281322	GM12891	blood:	n/a	n/a
11	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:228281005-228281316	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:228279745-228282720	K562	blood:	n/a	n/a
14	POLR2A	chr1:228279922-228281309	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:228279806-228282603	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:228280254-228281326	HL-60	blood:	n/a	n/a
17	POLR2A	chr1:228279814-228281389	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:228280898-228281286	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:228275014-228282866	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:228279821-228281368	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:228280081-228281290	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:228280043-228281427	K562	blood:	n/a	n/a
23	POLR2A	chr1:228276361-228281309	A549	lung:	n/a	n/a
24	POLR2A	chr1:228279831-228281377	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:228279792-228281560	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr1:228274271-228281353	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:228279831-228281430	GM12892	blood:	n/a	n/a
28	POLR2A	chr1:228280972-228281281	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr1:228279692-228281364	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228279258..228282133-chr1:228294135..228296002,2	MCF-7	breast:
2	chr1:228281021..228283258-chr1:228327400..228329608,2	MCF-7	breast:
3	chr1:228280178..228282214-chr1:228355468..228357999,2	K562	blood:

No data

Variant related genes	Relation type
MIR3620	TF binding region
ENSG00000143774	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10127654	1.00[AMR][1000 genomes]
rs11541554	1.00[AMR][1000 genomes]
rs15109	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16848270	1.00[ASN][1000 genomes]
rs2231717	1.00[AMR][1000 genomes]
rs3754359	0.92[AFR][1000 genomes]
rs55662277	1.00[AMR][1000 genomes]
rs55686465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55904630	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55923168	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56029925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56080014	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56137152	1.00[AMR][1000 genomes]
rs56280722	1.00[AMR][1000 genomes]
rs56285667	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56377909	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56386805	1.00[AMR][1000 genomes]
rs56410225	1.00[AMR][1000 genomes]
rs56831205	1.00[ASN][1000 genomes]
rs57446195	1.00[ASN][1000 genomes]
rs58045861	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59460700	1.00[AMR][1000 genomes]
rs59478442	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60245137	1.00[ASN][1000 genomes]
rs60628313	1.00[AMR][1000 genomes]
rs61100243	1.00[AMR][1000 genomes]
rs61230585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61401568	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61737797	1.00[ASN][1000 genomes]
rs74140905	0.92[AFR][1000 genomes]
rs74140907	1.00[ASN][1000 genomes]
rs74140910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140912	1.00[ASN][1000 genomes]
rs74140915	1.00[ASN][1000 genomes]
rs74140916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140918	1.00[ASN][1000 genomes]
rs74140919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140925	1.00[ASN][1000 genomes]
rs74140953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140960	1.00[ASN][1000 genomes]
rs74140961	1.00[ASN][1000 genomes]
rs74140962	0.92[AFR][1000 genomes]
rs74140963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140965	1.00[ASN][1000 genomes]
rs74140967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140968	0.92[AFR][1000 genomes]
rs74140969	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140970	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140972	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140973	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140974	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140975	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140976	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140977	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140978	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140980	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140981	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140985	0.85[AFR][1000 genomes]
rs74140986	1.00[AMR][1000 genomes]
rs74140987	1.00[AMR][1000 genomes]
rs74140988	1.00[AMR][1000 genomes]
rs74140989	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140990	1.00[AMR][1000 genomes]
rs74140994	0.90[ASN][1000 genomes]
rs74140996	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140999	1.00[AMR][1000 genomes]
rs74141000	1.00[AMR][1000 genomes]
rs74141002	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74142604	1.00[AMR][1000 genomes]
rs74142605	1.00[AMR][1000 genomes]
rs74142606	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74142608	0.90[ASN][1000 genomes]
rs74142610	1.00[AMR][1000 genomes]
rs74142611	1.00[AMR][1000 genomes]
rs74142613	1.00[AMR][1000 genomes]
rs74142618	1.00[AMR][1000 genomes]
rs74142619	1.00[AMR][1000 genomes]
rs74142622	1.00[AMR][1000 genomes]
rs74142625	0.90[ASN][1000 genomes]
rs74142626	1.00[AMR][1000 genomes]
rs74142627	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74142629	1.00[AMR][1000 genomes]
rs74142630	1.00[AMR][1000 genomes]
rs74142642	0.90[ASN][1000 genomes]
rs74142644	0.90[ASN][1000 genomes]
rs74142645	0.90[ASN][1000 genomes]
rs74142647	0.90[ASN][1000 genomes]
rs74143631	1.00[ASN][1000 genomes]
rs74143632	1.00[ASN][1000 genomes]
rs74143634	1.00[ASN][1000 genomes]
rs74143635	1.00[ASN][1000 genomes]
rs74143636	1.00[ASN][1000 genomes]
rs74143637	1.00[ASN][1000 genomes]
rs74143638	1.00[ASN][1000 genomes]
rs74143640	1.00[ASN][1000 genomes]
rs74143641	1.00[ASN][1000 genomes]
rs74143642	1.00[ASN][1000 genomes]
rs74143662	1.00[ASN][1000 genomes]
rs74143665	1.00[ASN][1000 genomes]
rs74143667	1.00[ASN][1000 genomes]
rs752108	1.00[ASN][1000 genomes]
rs752109	1.00[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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active 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 miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228273600-228281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:228275200-228282000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:228275400-228281400	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
8	chr1:228276000-228281400	Genic enhancers	Placenta	Placenta
9	chr1:228276400-228281400	Genic enhancers	Lung	lung
10	chr1:228276600-228281800	Weak transcription	Fetal Lung	lung
11	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:228276800-228281800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:228278000-228281400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
18	chr1:228278400-228281400	Genic enhancers	HMEC	breast
19	chr1:228278400-228282200	Weak transcription	Aorta	Aorta
20	chr1:228278600-228281800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:228278800-228282000	Strong transcription	NHDF-Ad	bronchial
22	chr1:228278800-228282800	ZNF genes & repeats	GM12878-XiMat	blood
23	chr1:228278800-228283000	ZNF genes & repeats	Dnd41	blood
24	chr1:228278800-228283600	Weak transcription	Ovary	ovary
25	chr1:228279000-228282200	Genic enhancers	Spleen	Spleen
26	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
27	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:228279400-228281400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:228279400-228281400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:228279400-228281600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:228279400-228283400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:228279400-228284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:228279600-228281800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:228279600-228281800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:228279600-228285600	Weak transcription	NH-A	brain
36	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr1:228279800-228281400	Enhancers	Esophagus	oesophagus
38	chr1:228279800-228281800	Weak transcription	Brain Substantia Nigra	brain
39	chr1:228279800-228282600	ZNF genes & repeats	K562	blood
40	chr1:228280000-228281400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:228280000-228281400	Genic enhancers	Left Ventricle	heart
42	chr1:228280000-228282000	Strong transcription	Primary T cells from cord blood	blood
43	chr1:228280000-228282000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:228280000-228282200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr1:228280000-228283600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:228280000-228283600	ZNF genes & repeats	Thymus	Thymus
47	chr1:228280000-228284000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:228280000-228284000	ZNF genes & repeats	Fetal Thymus	thymus
49	chr1:228280000-228284200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:228280000-228285200	ZNF genes & repeats	Fetal Stomach	stomach

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