Variant report

Variant	rs873532
Chromosome Location	chr2:46726629-46726630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:46726594-46727591	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:46726627-46727558	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr2:46725963-46728174	SK-N-SH	brain:	n/a	chr2:46727430-46727439

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:46705265..46709008-chr2:46724758..46728950,5	K562	blood:
2	chr2:46726104..46727862-chr2:46768328..46770840,3	MCF-7	breast:
3	chr2:46724562..46726815-chr2:46734008..46735625,2	MCF-7	breast:
4	chr2:46726438..46729524-chr2:46768838..46771074,3	K562	blood:
5	chr2:46724349..46729821-chr2:46769212..46772070,6	MCF-7	breast:
6	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGF-3	chr2:46726369-46727177	XLOC_002085
2	lnc-PIGF-3	chr2:46726542-46726918	XLOC_002085
3	lnc-PIGF-3	chr2:46726620-46726918	NONHSAT070504

No data

Variant related genes	Relation type
ENSG00000253515	TF binding region
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000187600	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs55680262	0.83[AFR][1000 genomes]
rs55770522	0.83[AFR][1000 genomes]
rs55775849	1.00[AFR][1000 genomes]
rs55857444	0.83[AFR][1000 genomes]
rs55939277	1.00[AFR][1000 genomes]
rs56194963	0.83[AFR][1000 genomes]
rs56290425	0.86[AFR][1000 genomes]
rs56365783	0.86[AFR][1000 genomes]
rs56678855	0.86[AFR][1000 genomes]
rs57134197	0.83[AFR][1000 genomes]
rs57453502	0.83[AFR][1000 genomes]
rs58143719	0.83[AFR][1000 genomes]
rs58395052	0.83[AFR][1000 genomes]
rs59253102	0.86[AFR][1000 genomes]
rs60086470	0.83[AFR][1000 genomes]
rs60100807	0.83[AFR][1000 genomes]
rs61065239	0.86[AFR][1000 genomes]
rs61169200	0.86[AFR][1000 genomes]
rs6756900	1.00[YRI][hapmap]
rs73927843	0.86[AFR][1000 genomes]
rs73927846	1.00[AFR][1000 genomes]
rs73927847	0.86[AFR][1000 genomes]
rs73927849	1.00[AFR][1000 genomes]
rs73927872	1.00[AFR][1000 genomes]
rs73927876	0.86[AFR][1000 genomes]
rs73929731	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1000129	chr2:46723102-46733814	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 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	chr2:46718800-46727000	Weak transcription	Spleen	Spleen
2	chr2:46726000-46727200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr2:46726400-46726800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr2:46726400-46726800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:46726400-46726800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr2:46726400-46726800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:46726400-46726800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr2:46726400-46726800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:46726400-46726800	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:46726400-46727200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:46726400-46727800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:46726600-46726800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:46726600-46726800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:46726600-46726800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:46726600-46726800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr2:46726600-46726800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:46726600-46726800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:46726600-46726800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:46726600-46726800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr2:46726600-46726800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:46726600-46726800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:46726600-46726800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:46726600-46726800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:46726600-46726800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
25	chr2:46726600-46726800	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:46726600-46726800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr2:46726600-46726800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:46726600-46726800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr2:46726600-46726800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:46726600-46726800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr2:46726600-46726800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:46726600-46726800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:46726600-46726800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:46726600-46726800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:46726600-46726800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:46726600-46726800	Enhancers	Liver	Liver
37	chr2:46726600-46726800	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr2:46726600-46726800	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr2:46726600-46726800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr2:46726600-46726800	Enhancers	Esophagus	oesophagus
41	chr2:46726600-46726800	Flanking Active TSS	Fetal Brain Female	brain
42	chr2:46726600-46726800	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr2:46726600-46726800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
44	chr2:46726600-46726800	Flanking Active TSS	Fetal Lung	lung
45	chr2:46726600-46726800	Bivalent Enhancer	Fetal Thymus	thymus
46	chr2:46726600-46726800	Flanking Active TSS	Left Ventricle	heart
47	chr2:46726600-46726800	Enhancers	Pancreas	Pancrea
48	chr2:46726600-46726800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr2:46726600-46726800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
50	chr2:46726600-46726800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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