Variant report

Variant	rs13007719
Chromosome Location	chr2:55848467-55848468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55847510-55848770	HepG2	liver:	n/a	n/a
2	CTCF	chr2:55848460-55848610	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:55848397-55848467	K562	blood:	n/a	n/a
4	POLR2A	chr2:55848466-55849792	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr2:55848337-55848558	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:55848173-55849329	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55818262..55820533-chr2:55847496..55849858,2	MCF-7	breast:
3	chr2:55843280..55846696-chr2:55847912..55852861,6	MCF-7	breast:
4	chr2:55847894..55850021-chr2:55856235..55857780,2	MCF-7	breast:
5	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:

No data

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000138041	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12623293	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12623937	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12987272	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12993839	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12994656	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12998664	0.93[AMR][1000 genomes]
rs13001452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13004436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13009649	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13015243	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13019595	0.81[AMR][1000 genomes]
rs13025994	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13030396	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542643	0.80[AMR][1000 genomes]
rs17737233	0.93[AMR][1000 genomes]
rs1867334	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2054729	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291336	0.81[AMR][1000 genomes]
rs34400247	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35057183	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35124901	0.81[AMR][1000 genomes]
rs35255044	0.91[AMR][1000 genomes]
rs35861320	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35968359	0.90[AMR][1000 genomes]
rs3748944	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3748952	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828238	0.81[AMR][1000 genomes]
rs6753530	0.90[AMR][1000 genomes]
rs878124	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55846600-55848600	Weak transcription	Esophagus	oesophagus
4	chr2:55846600-55848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:55846600-55849000	Enhancers	Colon Smooth Muscle	Colon
6	chr2:55846600-55850400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
14	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55846800-55848600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:55846800-55848600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:55846800-55848600	Weak transcription	Fetal Brain Female	brain
19	chr2:55846800-55848800	Enhancers	Adipose Nuclei	Adipose
20	chr2:55846800-55848800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:55846800-55848800	Enhancers	Pancreas	Pancrea
22	chr2:55846800-55850400	Enhancers	Liver	Liver
23	chr2:55846800-55851200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr2:55846800-55853000	Weak transcription	A549	lung
25	chr2:55846800-55858200	Weak transcription	HSMM	muscle
26	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
30	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
31	chr2:55846800-55863400	Weak transcription	NHLF	lung
32	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:55847000-55849400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55847000-55852600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr2:55847200-55849200	Weak transcription	Ovary	ovary
37	chr2:55847400-55848600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:55847400-55848800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:55847400-55849200	Genic enhancers	Lung	lung
40	chr2:55847400-55852400	Weak transcription	HMEC	breast
41	chr2:55847400-55852800	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:55847600-55848600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:55847600-55848600	Enhancers	Primary T cells from cord blood	blood
47	chr2:55847600-55848600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:55847600-55848600	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:55847600-55848600	Weak transcription	Left Ventricle	heart
50	chr2:55847600-55848600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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