Variant report

Variant	rs73416054
Chromosome Location	chr6:33381082-33381083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33380373-33382176	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:33380882-33381361	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:33379963-33384071	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr6:33380856-33381309	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:33380911-33381182	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:33379970-33384148	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:33380035-33383888	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr6:33380240-33381549	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr6:33380588-33381469	A549	lung:	n/a	n/a
10	POLR2A	chr6:33380484-33381251	MCF-7	breast:	n/a	n/a
11	POLR2A	chr6:33380137-33384099	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr6:33380905-33381164	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:33380867-33381651	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr6:33380874-33381407	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:33380085-33387208	IMR90	lung:	n/a	n/a
16	POLR2A	chr6:33380614-33382070	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:33380133-33382472	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:33381007-33381238	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr6:33380766-33381111	HCT-116	colon:	n/a	n/a
20	POLR2A	chr6:33380602-33381085	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:33380860-33381892	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:33380194-33381878	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr6:33380030-33382674	HepG2	liver:	n/a	n/a
24	POLR2A	chr6:33380383-33382359	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:33380060-33386533	K562	blood:	n/a	n/a
26	POLR2A	chr6:33380530-33381570	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr6:33381030-33381880	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:33380456-33382511	HepG2	liver:	n/a	n/a
29	POLR2A	chr6:33380895-33384143	K562	blood:	n/a	n/a
30	POLR2A	chr6:33380002-33384129	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr6:33380813-33381185	K562	blood:	n/a	n/a
32	POLR2A	chr6:33380737-33381578	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr6:33380853-33381975	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:33380920-33381132	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:33381024-33381299	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr6:33380390-33383943	K562	blood:	n/a	n/a
37	POLR2A	chr6:33380708-33381973	K562	blood:	n/a	n/a
38	POLR2A	chr6:33380824-33381908	HL-60	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
3	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
4	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
5	chr12:121908083..121909947-chr6:33379733..33381341,2	MCF-7	breast:
6	chr6:33244680..33251060-chr6:33375427..33382644,12	MCF-7	breast:
7	chr6:33238401..33240913-chr6:33381042..33383923,3	MCF-7	breast:

No data

Variant related genes	Relation type
PHF1	TF binding region
ENSG00000231500	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000204209	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs56957947	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57206692	0.86[AFR][1000 genomes]
rs57745261	0.81[AFR][1000 genomes]
rs57991968	0.86[AFR][1000 genomes]
rs58287097	0.82[AFR][1000 genomes]
rs59507163	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60023810	1.00[AMR][1000 genomes]
rs6901048	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402303	0.86[AFR][1000 genomes]
rs73402305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402312	0.83[AFR][1000 genomes]
rs73402320	0.83[AFR][1000 genomes]
rs73412030	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469425	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33379600-33381200	Weak transcription	Small Intestine	intestine
2	chr6:33379600-33381200	Weak transcription	HUVEC	blood vessel
3	chr6:33379600-33381800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:33379600-33384200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:33379600-33384400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:33379600-33384400	Weak transcription	Fetal Kidney	kidney
7	chr6:33379600-33384400	Weak transcription	Stomach Mucosa	stomach
8	chr6:33379800-33381200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:33379800-33381400	Weak transcription	A549	lung
10	chr6:33379800-33382600	Weak transcription	Fetal Brain Male	brain
11	chr6:33379800-33383200	Genic enhancers	NHDF-Ad	bronchial
12	chr6:33379800-33383600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:33379800-33384200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:33379800-33384200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:33379800-33384400	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr6:33380000-33381200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:33380000-33381200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:33380000-33381200	Genic enhancers	Adipose Nuclei	Adipose
19	chr6:33380000-33381200	Genic enhancers	Right Ventricle	heart
20	chr6:33380000-33381600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:33380000-33381800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:33380000-33382000	Strong transcription	Psoas Muscle	Psoas
23	chr6:33380000-33383000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:33380000-33383000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:33380000-33383200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:33380000-33383400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:33380000-33383400	Strong transcription	Fetal Thymus	thymus
28	chr6:33380000-33383600	Genic enhancers	Dnd41	blood
29	chr6:33380000-33383800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:33380000-33384000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:33380000-33384200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:33380000-33384400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:33380000-33384400	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr6:33380000-33384400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:33380000-33384600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
36	chr6:33380200-33381200	Genic enhancers	Rectal Mucosa Donor 31	rectum
37	chr6:33380200-33381400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
38	chr6:33380200-33381400	Strong transcription	GM12878-XiMat	blood
39	chr6:33380200-33381800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:33380200-33381800	Genic enhancers	Brain Anterior Caudate	brain
41	chr6:33380200-33381800	Strong transcription	Brain Germinal Matrix	brain
42	chr6:33380200-33381800	Genic enhancers	Fetal Brain Female	brain
43	chr6:33380200-33382000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:33380200-33382000	Genic enhancers	Gastric	stomach
45	chr6:33380200-33382000	Strong transcription	HSMMtube	muscle
46	chr6:33380200-33382200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:33380200-33382200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:33380200-33382400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:33380200-33382400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr6:33380200-33382600	Strong transcription	Fetal Lung	lung

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