Variant report

Variant	rs3219486
Chromosome Location	chr1:45799912-45799913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45799869-45800177	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45476992..45479513-chr1:45797519..45802277,7	K562	blood:
2	chr1:45798786..45801667-chr1:45804000..45806421,3	MCF-7	breast:
3	chr1:45476992..45480023-chr1:45798913..45801605,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TESK2-2	chr1:45799772-45800183	NONHSAT002936

No data

Variant related genes	Relation type
MUTYH	TF binding region
ENSG00000126088	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000132773	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17399402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3219474	1.00[AFR][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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45792400-45800600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:45792800-45804800	Weak transcription	Fetal Kidney	kidney
3	chr1:45792800-45805000	Weak transcription	HSMMtube	muscle
4	chr1:45793200-45804800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:45793400-45803800	Weak transcription	Small Intestine	intestine
6	chr1:45793400-45804000	Weak transcription	HMEC	breast
7	chr1:45793400-45805000	Weak transcription	Right Atrium	heart
8	chr1:45793600-45800600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:45793600-45800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:45793600-45803600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:45793600-45803600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:45793600-45804200	Weak transcription	Fetal Brain Male	brain
13	chr1:45793800-45803800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:45794000-45800000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:45794000-45800200	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:45794000-45800600	Strong transcription	Fetal Stomach	stomach
17	chr1:45794400-45800000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:45794400-45800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:45794400-45800400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:45794400-45800600	Strong transcription	Aorta	Aorta
21	chr1:45794400-45800800	Strong transcription	Fetal Brain Female	brain
22	chr1:45794600-45800000	Strong transcription	Primary T cells from cord blood	blood
23	chr1:45794600-45800400	Strong transcription	Pancreas	Pancrea
24	chr1:45794600-45800600	Strong transcription	Thymus	Thymus
25	chr1:45794800-45800200	Strong transcription	Brain Germinal Matrix	brain
26	chr1:45794800-45801200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:45795000-45800000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:45795000-45800000	Strong transcription	Liver	Liver
29	chr1:45795000-45800200	Strong transcription	Ovary	ovary
30	chr1:45795000-45800600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:45795000-45800600	Strong transcription	Dnd41	blood
32	chr1:45795400-45800000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:45795400-45800200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:45795400-45800200	Weak transcription	GM12878-XiMat	blood
35	chr1:45795400-45800600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr1:45795400-45800600	Strong transcription	Fetal Thymus	thymus
37	chr1:45795400-45801200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:45795600-45800000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:45795600-45800200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:45795600-45800200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:45795600-45800200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:45795600-45800200	Strong transcription	NHEK	skin
43	chr1:45795600-45800400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:45795600-45800600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr1:45795600-45800600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:45795600-45804400	Weak transcription	A549	lung
47	chr1:45795600-45804800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr1:45795800-45800200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:45795800-45800200	Strong transcription	Brain Angular Gyrus	brain
50	chr1:45795800-45800400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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