Variant report

Variant	rs73840260
Chromosome Location	chr3:53268003-53268004
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53267840-53268171	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:53267711-53269219	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:53267840-53268170	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:53267826-53268018	A549	lung:	n/a	n/a
5	POLR2A	chr3:53267871-53268766	K562	blood:	n/a	n/a
6	POLR2A	chr3:53261891-53271225	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:53267727-53268423	K562	blood:	n/a	n/a
8	POLR2A	chr3:53267811-53269199	GM12891	blood:	n/a	n/a
9	POLR2A	chr3:53267803-53269230	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:53267851-53268004	A549	lung:	n/a	n/a
11	POLR2A	chr3:53267905-53268165	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr3:53267768-53268241	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:53264706-53269099	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:53261940-53270977	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:53267886-53268590	K562	blood:	n/a	n/a
16	NFATC1	chr3:53267904-53268244	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:53267739-53269221	K562	blood:	n/a	n/a
18	POLR2A	chr3:53267925-53269066	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:53267857-53268020	A549	lung:	n/a	n/a
20	POLR2A	chr3:53267888-53268622	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:53267691-53269000	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr3:53267847-53268676	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:53267920-53268120	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:53267878-53268615	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:53267728-53271263	GM12892	blood:	n/a	n/a
26	POLR2A	chr3:53264807-53269247	HL-60	blood:	n/a	n/a
27	POLR2A	chr3:53267882-53268064	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:53267806-53268624	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:53253532-53269075	A549	lung:	n/a	n/a
30	POLR2A	chr3:53255471-53271280	K562	blood:	n/a	n/a
31	POLR2A	chr3:53267836-53268761	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:53267828-53268189	A549	lung:	n/a	n/a
33	POLR2A	chr3:53267824-53269037	GM12892	blood:	n/a	n/a
34	POLR2A	chr3:53266620-53268457	K562	blood:	n/a	n/a
35	POLR2A	chr3:53267721-53271338	HL-60	blood:	n/a	n/a
36	POLR2A	chr3:53267775-53268662	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr3:53267957-53268571	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:53267823-53269792	GM12892	blood:	n/a	n/a
39	POLR2A	chr3:53267747-53268583	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:53266535..53268098-chr3:53269549..53272013,3	K562	blood:
2	chr3:53267066..53270422-chr3:53274180..53278623,4	K562	blood:
3	chr3:53266350..53272175-chr3:53273806..53279972,8	K562	blood:

No data

Variant related genes	Relation type
TKT	TF binding region
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs55739626	1.00[AMR][1000 genomes]
rs55797425	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56138740	1.00[AMR][1000 genomes]
rs57085673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57188310	1.00[AMR][1000 genomes]
rs57320366	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57530569	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58006923	1.00[AMR][1000 genomes]
rs58191586	1.00[AMR][1000 genomes]
rs58563464	1.00[AMR][1000 genomes]
rs60407612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60891705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957562	1.00[AMR][1000 genomes]
rs73840218	1.00[AMR][1000 genomes]
rs73840219	1.00[AMR][1000 genomes]
rs73840220	1.00[AMR][1000 genomes]
rs73840224	1.00[AMR][1000 genomes]
rs73840228	1.00[AMR][1000 genomes]
rs73840236	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73840239	1.00[AMR][1000 genomes]
rs73840247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73840281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73840298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843108	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843110	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843111	1.00[AMR][1000 genomes]
rs73843112	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843113	1.00[AMR][1000 genomes]
rs73843115	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843117	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843118	0.93[AFR][1000 genomes]
rs73843120	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843121	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843124	1.00[AMR][1000 genomes]
rs73843127	1.00[AMR][1000 genomes]
rs73843129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843130	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73843148	1.00[AMR][1000 genomes]
rs874586	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53229000-53270000	Weak transcription	Right Atrium	heart
2	chr3:53254400-53270400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:53255600-53274400	Strong transcription	GM12878-XiMat	blood
4	chr3:53255800-53269800	Genic enhancers	A549	lung
5	chr3:53255800-53269800	Strong transcription	Osteobl	bone
6	chr3:53256000-53269600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:53256000-53269600	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr3:53256000-53269600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:53256200-53269000	Strong transcription	Right Ventricle	heart
10	chr3:53256200-53269600	Strong transcription	Fetal Intestine Small	intestine
11	chr3:53256200-53269600	Strong transcription	NHLF	lung
12	chr3:53256200-53270000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:53256200-53270000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:53256200-53270000	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:53256400-53269400	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:53256400-53269600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:53256400-53270000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:53256400-53270000	Weak transcription	Fetal Kidney	kidney
19	chr3:53256400-53270000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr3:53256400-53270200	Strong transcription	Fetal Thymus	thymus
21	chr3:53256400-53272400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:53256400-53276400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:53256400-53276600	Strong transcription	Fetal Brain Female	brain
24	chr3:53256400-53276800	Strong transcription	Fetal Stomach	stomach
25	chr3:53256600-53268400	Strong transcription	Esophagus	oesophagus
26	chr3:53256600-53269600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:53256600-53270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:53256600-53270000	Strong transcription	Lung	lung
29	chr3:53256600-53272000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:53256800-53269000	Strong transcription	Liver	Liver
31	chr3:53256800-53269600	Strong transcription	HMEC	breast
32	chr3:53256800-53269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:53256800-53270000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:53256800-53270000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr3:53256800-53272200	Strong transcription	Brain Germinal Matrix	brain
36	chr3:53256800-53276600	Strong transcription	Thymus	Thymus
37	chr3:53256800-53277000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:53256800-53277000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:53257000-53269600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:53257000-53270400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:53257000-53270600	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr3:53257000-53276800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:53257000-53276800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:53257000-53277800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:53257200-53269600	Strong transcription	NHDF-Ad	bronchial
46	chr3:53257200-53270000	Strong transcription	Brain Anterior Caudate	brain
47	chr3:53257200-53270000	Strong transcription	Gastric	stomach
48	chr3:53257200-53270200	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr3:53257200-53271000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:53257200-53276200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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