Variant report

Variant	rs28538473
Chromosome Location	chr2:46796075-46796076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46769044..46771933-chr2:46795077..46797963,2	MCF-7	breast:
2	chr2:46795284..46799480-chr2:46800888..46803285,4	K562	blood:
3	chr2:46794873..46797184-chr2:46839917..46841642,2	K562	blood:
4	chr2:46789524..46792081-chr2:46795199..46798160,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGF-1	chr2:46795395-46796709	ENSG00000250116.2
2	lnc-PIGF-1	chr2:46795376-46796709	NONHSAT070512
3	lnc-PIGF-1	chr2:46795396-46796709	NR_104182

No data

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1901262	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61615640	0.92[EUR][1000 genomes]
rs7599922	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:46772200-46804000	Weak transcription	NH-A	brain
3	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
5	chr2:46782200-46798400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
7	chr2:46782800-46803600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:46783000-46796800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:46783200-46803000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:46784000-46802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:46785400-46798400	Weak transcription	Liver	Liver
14	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:46785600-46796400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:46785600-46803800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:46786800-46805200	Weak transcription	Small Intestine	intestine
19	chr2:46787200-46799800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:46787800-46806600	Weak transcription	Gastric	stomach
21	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
22	chr2:46789600-46796400	Weak transcription	Pancreas	Pancrea
23	chr2:46789800-46796600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:46789800-46805800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:46789800-46807000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:46790000-46803400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:46790000-46803800	Weak transcription	Primary T cells from cord blood	blood
28	chr2:46790000-46807200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:46790200-46803400	Weak transcription	A549	lung
31	chr2:46790200-46807000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:46790200-46807400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:46790600-46803800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:46790600-46806200	Weak transcription	Dnd41	blood
35	chr2:46791400-46796800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:46792200-46809200	Weak transcription	Esophagus	oesophagus
37	chr2:46792600-46796200	Weak transcription	Thymus	Thymus
38	chr2:46793000-46803800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:46793000-46806400	Weak transcription	Lung	lung
40	chr2:46793200-46806200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:46793200-46806200	Weak transcription	Aorta	Aorta
42	chr2:46793400-46799800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:46794000-46800200	Enhancers	Primary hematopoietic stem cells	blood
44	chr2:46794200-46796200	Enhancers	Primary B cells from cord blood	blood
45	chr2:46794200-46796400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:46794400-46796200	Enhancers	Right Atrium	heart
47	chr2:46794400-46799600	Enhancers	Fetal Thymus	thymus
48	chr2:46794600-46797800	Enhancers	HSMMtube	muscle
49	chr2:46794600-46800000	Enhancers	Ovary	ovary
50	chr2:46794800-46796600	Enhancers	Brain Substantia Nigra	brain

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